SEC Info  
    Home      Search      My Interests      Help      Sign In      Please Sign In
 
We’re going down soon, to move to a new Data Center today.  We’ll be up ASAP.  Sorry.

Codexis, Inc. – ‘10-K’ for 12/31/23 – ‘EX-101.DEF’

On:  Wednesday, 2/28/24, at 4:37pm ET   ·   For:  12/31/23   ·   Accession #:  1200375-24-9   ·   File #:  1-34705

Previous ‘10-K’:  ‘10-K’ on 2/27/23 for 12/31/22   ·   Latest ‘10-K’:  This Filing   ·   27 References:   

Find Words in Filings emoji
 
  in    Show  and   Hints

  As Of               Filer                 Filing    For·On·As Docs:Size

 2/28/24  Codexis, Inc.                     10-K       12/31/23  121:13M

Annual Report   —   Form 10-K   —   SEA’34

Filing Table of Contents

Document/Exhibit                   Description                      Pages   Size 

 1: 10-K        Annual Report                                       HTML   2.18M 
 2: EX-4.4      Instrument Defining the Rights of Security Holders  HTML     50K 
 3: EX-10.11    Material Contract                                   HTML    836K 
 4: EX-10.17    Material Contract                                   HTML    535K 
 5: EX-23.1     Consent of Expert or Counsel                        HTML     33K 
 9: EX-97.1     Clawback Policy re: Recovery of Erroneously         HTML     42K 
                Awarded Compensation                                             
 6: EX-31.1     Certification -- §302 - SOA'02                      HTML     37K 
 7: EX-31.2     Certification -- §302 - SOA'02                      HTML     37K 
 8: EX-32.1     Certification -- §906 - SOA'02                      HTML     34K 
15: R1          Cover Page                                          HTML     99K 
16: R2          Audit Information                                   HTML     38K 
17: R3          Consolidated Balance Sheets                         HTML    154K 
18: R4          Consolidated Balance Sheets (Parenthetical)         HTML     55K 
19: R5          Consolidated Statements of Operations               HTML    105K 
20: R6          Consolidated Statements of Operations               HTML     45K 
                (Parenthetical)                                                  
21: R7          Consolidated Statements of Stockholders' Equity     HTML     90K 
22: R8          Consolidated Statements of Stockholders' Equity     HTML     34K 
                (Parenthetical)                                                  
23: R9          Consolidated Statements of Cash Flows               HTML    133K 
24: R10         Consolidated Statements of Cash Flows               HTML     43K 
                (Parenthetical)                                                  
25: R11         Description of Business                             HTML     38K 
26: R12         Basis of Presentation and Summary of Significant    HTML    106K 
                Accounting Policies                                              
27: R13         Revenue Recognition                                 HTML     83K 
28: R14         Net Loss per Share                                  HTML     42K 
29: R15         Collaborative Arrangements                          HTML     80K 
30: R16         Investments in Non-Marketable Securities            HTML     52K 
31: R17         Fair Value Measurements                             HTML     46K 
32: R18         Balance Sheet Details                               HTML     84K 
33: R19         Stock-based Compensation                            HTML    201K 
34: R20         Capital Stock                                       HTML     42K 
35: R21         401(k) Plan                                         HTML     38K 
36: R22         Income Taxes                                        HTML    122K 
37: R23         Commitments and Contingencies                       HTML     93K 
38: R24         Related Party Transactions                          HTML     41K 
39: R25         Segment, Geographical and Other Revenue             HTML     78K 
                Information                                                      
40: R26         Allowance for Credit Losses                         HTML     63K 
41: R27         Restructuring Charges                               HTML     38K 
42: R28         Subsequent Events                                   HTML     36K 
43: R29         Pay vs Performance Disclosure                       HTML     45K 
44: R30         Insider Trading Arrangements                        HTML     39K 
45: R31         Basis of Presentation and Summary of Significant    HTML    163K 
                Accounting Policies (Policies)                                   
46: R32         Basis of Presentation and Summary of Significant    HTML     55K 
                Accounting Policies (Tables)                                     
47: R33         Revenue Recognition (Tables)                        HTML     79K 
48: R34         Net Loss per Share (Tables)                         HTML     39K 
49: R35         Investments in Non-Marketable Securities (Tables)   HTML     42K 
50: R36         Fair Value Measurements (Tables)                    HTML     47K 
51: R37         Balance Sheet Details (Tables)                      HTML     94K 
52: R38         Stock-based Compensation (Tables)                   HTML    193K 
53: R39         Income Taxes (Tables)                               HTML    125K 
54: R40         Commitments and Contingencies (Tables)              HTML     86K 
55: R41         Segment, Geographical and Other Revenue             HTML     80K 
                Information (Tables)                                             
56: R42         Allowance for Credit Losses (Tables)                HTML     64K 
57: R43         Description of Business (Details)                   HTML     35K 
58: R44         Basis of Presentation and Summary of Significant    HTML     66K 
                Accounting Policies - Narrative (Details)                        
59: R45         Basis of Presentation and Summary of Significant    HTML     40K 
                Accounting Policies - Property, Plant, and                       
                Equipment (Details)                                              
60: R46         Revenue Recognition - Disaggregation of Revenue     HTML     51K 
                (Details)                                                        
61: R47         Revenue Recognition - Contracts with Customer       HTML     42K 
                (Details)                                                        
62: R48         Revenue Recognition - Narrative (Details)           HTML     51K 
63: R49         Revenue Recognition - Revenue Recognized (Details)  HTML     43K 
64: R50         Revenue Recognition - Performance Obligation        HTML     49K 
                (Details)                                                        
65: R51         Net Loss per Share (Details)                        HTML     40K 
66: R52         Collaborative Arrangements - GSK Platform           HTML     50K 
                Technology Transfer, Collaboration and License                   
                Agreement (Details)                                              
67: R53         Collaborative Arrangements - Merck Platform         HTML     44K 
                Technology Transfer and License Agreement                        
                (Details)                                                        
68: R54         Collaborative Arrangements - Merck Sitagliptin      HTML     60K 
                Catalyst Supply Agreement (Details)                              
69: R55         Collaborative Arrangements - Enzyme Supply          HTML     49K 
                Agreement (Details)                                              
70: R56         Collaborative Arrangements - Commercial Agreement   HTML     39K 
                (Details)                                                        
71: R57         Collaborative Arrangements - Global Development,    HTML     42K 
                Option and License Agreement and Strategic                       
                Collaboration Agreement (Details)                                
72: R58         Collaborative Arrangements - Acquisition Agreement  HTML     46K 
                (Details)                                                        
73: R59         Collaborative Arrangements - Strategic              HTML     54K 
                Collaboration Agreement (Details)                                
74: R60         Collaborative Arrangements - Platform Technology    HTML     59K 
                Transfer and License Agreement (Details)                         
75: R61         Collaborative Arrangements - License Agreement      HTML     50K 
                (Details)                                                        
76: R62         Collaborative Arrangements - Strategic              HTML     47K 
                Collaboration and License Agreement (Details)                    
77: R63         Collaborative Arrangements - Master Collaboration   HTML     73K 
                and Research Agreement, Stock Purchase Agreement                 
                and Enzyme Supply Agreement (Details)                            
78: R64         Collaborative Arrangements - Pfizer Enzyme Supply   HTML     68K 
                Agreement (Details)                                              
79: R65         Investments in Non-Marketable Securities -          HTML    143K 
                Narrative (Details)                                              
80: R66         Investments in Non-Marketable Securities -          HTML     45K 
                Carrying Value and Fair Value of Securities                      
                (Details)                                                        
81: R67         Fair Value Measurements (Details)                   HTML     49K 
82: R68         Balance Sheet Details - Cash and Cash Equivalents   HTML     40K 
                (Details)                                                        
83: R69         Balance Sheet Details - Narrative (Details)         HTML     61K 
84: R70         Balance Sheet Details - Schedule of Inventory       HTML     41K 
                Components (Details)                                             
85: R71         Balance Sheet Details - Property and Equipment,     HTML     57K 
                net (Details)                                                    
86: R72         Balance Sheet Details - Schedule of Goodwill        HTML     39K 
                (Details)                                                        
87: R73         Balance Sheet Details - Other Accrued Liabilities   HTML     40K 
                (Details)                                                        
88: R74         Stock-based Compensation - Narrative (Details)      HTML    194K 
89: R75         Stock-based Compensation - Stock-Based              HTML     52K 
                Compensation Expense (Details)                                   
90: R76         Stock-based Compensation - Assumptions Used         HTML     63K 
                (Details)                                                        
91: R77         Stock-based Compensation - Option Activity          HTML     83K 
                (Details)                                                        
92: R78         Stock-based Compensation - Award Activity           HTML    115K 
                (Details)                                                        
93: R79         Capital Stock (Details)                             HTML     60K 
94: R80         401(k) Plan (Details)                               HTML     34K 
95: R81         Income Taxes - Components of Loss Before Provision  HTML     42K 
                for Income Taxes (Details)                                       
96: R82         Income Taxes - Components of Provision for Income   HTML     52K 
                Taxes (Details)                                                  
97: R83         Income Taxes - Tax Rate Reconciliation (Details)    HTML     55K 
98: R84         Income Taxes - Components of Deferred Tax Assets    HTML     74K 
                and Liabilities (Details)                                        
99: R85         Income Taxes - Narrative (Details)                  HTML     45K 
100: R86         Income Taxes - NOL Carryforwards and Federal        HTML     42K  
                Research and Development Tax Credits (Details)                   
101: R87         Income Taxes - Reconciliation of Unrecognized Tax   HTML     42K  
                Benefits (Details)                                               
102: R88         Commitments and Contingencies - Narrative           HTML     94K  
                (Details)                                                        
103: R89         Commitment and Contingencies - Schedule of          HTML     51K  
                Right-of-use Assets and Lease Obligations                        
                (Details)                                                        
104: R90         Commitments and Contingencies - Lease Costs         HTML     43K  
                (Details)                                                        
105: R91         Commitments and Contingencies - Other Lease         HTML     45K  
                Information (Details)                                            
106: R92         Commitments and Contingencies - Maturity Analysis   HTML     56K  
                of Operating Lease (Details)                                     
107: R93         Commitments and Contingencies - Other Commitments   HTML     39K  
                (Details)                                                        
108: R94         Related Party Transactions (Details)                HTML     55K  
109: R95         Segment, Geographical and Other Revenue             HTML     36K  
                Information - Narrative (Details)                                
110: R96         Segment, Geographical and Other Revenue             HTML     55K  
                Information - Concentration Risk (Details)                       
111: R97         Segment, Geographical and Other Revenue             HTML     54K  
                Information - Revenues (Details)                                 
112: R98         Segment, Geographical and Other Revenue             HTML     39K  
                Information - Goodwill (Details)                                 
113: R99         Allowance for Credit Losses - Analysis of           HTML     41K  
                Allowance for Credit Losses (Details)                            
114: R100        Allowance for Credit Losses - Summary of Accounts   HTML     47K  
                Receivable by Aging Category (Details)                           
115: R101        Restructuring Charges (Details)                     HTML     45K  
116: R102        Subsequent Events (Details)                         HTML     61K  
118: XML         IDEA XML File -- Filing Summary                      XML    220K  
121: XML         XBRL Instance -- cdxs-20231231_htm                   XML   2.59M  
117: EXCEL       IDEA Workbook of Financial Report Info              XLSX    245K  
11: EX-101.CAL  XBRL Calculations -- cdxs-20231231_cal               XML    220K 
12: EX-101.DEF  XBRL Definitions -- cdxs-20231231_def                XML   1.10M 
13: EX-101.LAB  XBRL Labels -- cdxs-20231231_lab                     XML   2.54M 
14: EX-101.PRE  XBRL Presentations -- cdxs-20231231_pre              XML   1.72M 
10: EX-101.SCH  XBRL Schema -- cdxs-20231231                         XSD    255K 
119: JSON        XBRL Instance as JSON Data -- MetaLinks              675±  1.00M  
120: ZIP         XBRL Zipped Folder -- 0001200375-24-000009-xbrl      Zip    988K  


‘EX-101.DEF’   —   XBRL Definitions — cdxs-20231231_def


This Exhibit is an XBRL File.


                                                                                                                                                                                
<?xml version="1.0" encoding="windows-1252"?>
<!-- XBRL Document Created with the Workiva Platform -->
<!-- Copyright 2024 Workiva -->
<!-- r:94d45509-9aef-44d3-a47e-c1e1904e3223,g:402e078b-413f-4095-9479-d13944eb3b89 -->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
<link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/all" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all"/>
<link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension"/>
<link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default"/>
<link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain"/>
<link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member"/>
<link:roleRef roleURI="http://www.codexis.com/role/ConsolidatedBalanceSheetsParenthetical" xlink:type="simple" xlink:href="cdxs-20231231.xsd#ConsolidatedBalanceSheetsParenthetical"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/ConsolidatedBalanceSheetsParenthetical" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementTable_4fe1ac98-3083-4d82-ba15-a139c6af7234" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_StatementTable_4fe1ac98-3083-4d82-ba15-a139c6af7234" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_0b00d090-4518-4d90-b737-a6eca340c36c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_4fe1ac98-3083-4d82-ba15-a139c6af7234" xlink:to="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_0b00d090-4518-4d90-b737-a6eca340c36c" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_0b00d090-4518-4d90-b737-a6eca340c36c_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_0b00d090-4518-4d90-b737-a6eca340c36c" xlink:to="loc_us-gaap_RelatedPartyDomain_0b00d090-4518-4d90-b737-a6eca340c36c_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_8d7e2619-621c-4de5-b0d0-24658d30a3be" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_0b00d090-4518-4d90-b737-a6eca340c36c" xlink:to="loc_us-gaap_RelatedPartyDomain_8d7e2619-621c-4de5-b0d0-24658d30a3be" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyMember_60bfac0b-5e3b-4320-ac9c-cc61fce1541f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyDomain_8d7e2619-621c-4de5-b0d0-24658d30a3be" xlink:to="loc_us-gaap_RelatedPartyMember_60bfac0b-5e3b-4320-ac9c-cc61fce1541f" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_c7b2ad1b-2e57-48ab-b7da-b2abf9d3e18e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_c7b2ad1b-2e57-48ab-b7da-b2abf9d3e18e" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PreferredStockParOrStatedValuePerShare_1c23ad9e-9f85-4d8a-9d07-22975ffe332b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PreferredStockParOrStatedValuePerShare"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_PreferredStockParOrStatedValuePerShare_1c23ad9e-9f85-4d8a-9d07-22975ffe332b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PreferredStockSharesAuthorized_73e380d9-55a7-4c66-9654-b38e13ed1554" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PreferredStockSharesAuthorized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_PreferredStockSharesAuthorized_73e380d9-55a7-4c66-9654-b38e13ed1554" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PreferredStockSharesIssued_6aec161c-6f93-435a-8405-1e5df5c0ed74" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PreferredStockSharesIssued"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_PreferredStockSharesIssued_6aec161c-6f93-435a-8405-1e5df5c0ed74" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PreferredStockSharesOutstanding_e8224aa8-16c9-4b41-9ac6-c6b8e22839ad" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PreferredStockSharesOutstanding"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_PreferredStockSharesOutstanding_e8224aa8-16c9-4b41-9ac6-c6b8e22839ad" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockParOrStatedValuePerShare_4dc5ca7c-6c03-4b8a-be7b-1f256c184a30" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockParOrStatedValuePerShare"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_CommonStockParOrStatedValuePerShare_4dc5ca7c-6c03-4b8a-be7b-1f256c184a30" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockSharesAuthorized_e6a99414-6784-43fa-8522-2cd0929fdbff" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockSharesAuthorized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_CommonStockSharesAuthorized_e6a99414-6784-43fa-8522-2cd0929fdbff" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockSharesIssued_93394fe6-1773-4e1e-b9ca-184eae7f10d5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockSharesIssued"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_CommonStockSharesIssued_93394fe6-1773-4e1e-b9ca-184eae7f10d5" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockSharesOutstanding_fb03801f-ea62-4042-9821-aeb8f7e12939" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockSharesOutstanding"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_69f81b76-a3d7-4f98-b7e3-f7f39a0ceaff" xlink:to="loc_us-gaap_CommonStockSharesOutstanding_fb03801f-ea62-4042-9821-aeb8f7e12939" xlink:type="arc" order="8"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/ConsolidatedStatementsofOperations" xlink:type="simple" xlink:href="cdxs-20231231.xsd#ConsolidatedStatementsofOperations"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/ConsolidatedStatementsofOperations" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementTable_f1b066f4-e525-4ae8-aefd-45ad628e5619" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_StatementTable_f1b066f4-e525-4ae8-aefd-45ad628e5619" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_465de5f6-3665-41b1-95f8-606c1f24f623" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_f1b066f4-e525-4ae8-aefd-45ad628e5619" xlink:to="loc_srt_ProductOrServiceAxis_465de5f6-3665-41b1-95f8-606c1f24f623" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_465de5f6-3665-41b1-95f8-606c1f24f623_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_465de5f6-3665-41b1-95f8-606c1f24f623" xlink:to="loc_srt_ProductsAndServicesDomain_465de5f6-3665-41b1-95f8-606c1f24f623_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_b48e70d0-d9e0-4caa-99a4-12442a083c6b" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_465de5f6-3665-41b1-95f8-606c1f24f623" xlink:to="loc_srt_ProductsAndServicesDomain_b48e70d0-d9e0-4caa-99a4-12442a083c6b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_13e87bfe-26d7-428b-8bca-1190f416711e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_b48e70d0-d9e0-4caa-99a4-12442a083c6b" xlink:to="loc_us-gaap_ProductMember_13e87bfe-26d7-428b-8bca-1190f416711e" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_06e9de3c-eb7b-41ee-91f9-1c0d0e94fba4" xlink:href="cdxs-20231231.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_b48e70d0-d9e0-4caa-99a4-12442a083c6b" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_06e9de3c-eb7b-41ee-91f9-1c0d0e94fba4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenuesAbstract_e07e4c44-1945-4e07-854a-d3eab65cf2e3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenuesAbstract"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_RevenuesAbstract_e07e4c44-1945-4e07-854a-d3eab65cf2e3" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_f50d95ea-eb92-4ad2-a902-d1dcc1a7f926" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RevenuesAbstract_e07e4c44-1945-4e07-854a-d3eab65cf2e3" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_f50d95ea-eb92-4ad2-a902-d1dcc1a7f926" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OperatingCostsAndExpensesAbstract"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CostOfGoodsAndServicesSold_6d61a76c-1b26-4838-9f4a-396ffc075659" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CostOfGoodsAndServicesSold"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:to="loc_us-gaap_CostOfGoodsAndServicesSold_6d61a76c-1b26-4838-9f4a-396ffc075659" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentExpense_f87a8155-1921-4e4c-8c10-25873a346acb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:to="loc_us-gaap_ResearchAndDevelopmentExpense_f87a8155-1921-4e4c-8c10-25873a346acb" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SellingGeneralAndAdministrativeExpense_fd86ca7a-cb66-4b65-8876-99e04ed2aab3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SellingGeneralAndAdministrativeExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:to="loc_us-gaap_SellingGeneralAndAdministrativeExpense_fd86ca7a-cb66-4b65-8876-99e04ed2aab3" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestructuringCharges_f732a0a7-96e1-4b6e-b2c3-d8890394536d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestructuringCharges"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:to="loc_us-gaap_RestructuringCharges_f732a0a7-96e1-4b6e-b2c3-d8890394536d" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_AssetImpairmentAndOtherCharges_75eb4d31-7301-44d5-92bd-101aacf2e123" xlink:href="cdxs-20231231.xsd#cdxs_AssetImpairmentAndOtherCharges"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:to="loc_cdxs_AssetImpairmentAndOtherCharges_75eb4d31-7301-44d5-92bd-101aacf2e123" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CostsAndExpenses_0b242010-4b3a-40f0-a2f6-bfe79440ec73" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CostsAndExpenses"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_b1505a55-463f-432f-9a3a-6ee2ce63ff2f" xlink:to="loc_us-gaap_CostsAndExpenses_0b242010-4b3a-40f0-a2f6-bfe79440ec73" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingIncomeLoss_bfb9466c-dc9f-45f8-9ad0-11990ca650b8" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OperatingIncomeLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_OperatingIncomeLoss_bfb9466c-dc9f-45f8-9ad0-11990ca650b8" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentIncomeInterest_fee4d485-6ec1-44a5-bbaa-fc95672ffd71" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_InvestmentIncomeInterest"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_InvestmentIncomeInterest_fee4d485-6ec1-44a5-bbaa-fc95672ffd71" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherNonoperatingIncomeExpense_dee68f11-59fc-4a66-a453-c4ca1827f982" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherNonoperatingIncomeExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_OtherNonoperatingIncomeExpense_dee68f11-59fc-4a66-a453-c4ca1827f982" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest_666946e0-280a-4a2a-b49f-54d9b09e0bbf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest_666946e0-280a-4a2a-b49f-54d9b09e0bbf" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeTaxExpenseBenefit_fcff18f3-5614-4164-aff2-3c1e2a0ac850" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeTaxExpenseBenefit"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_IncomeTaxExpenseBenefit_fcff18f3-5614-4164-aff2-3c1e2a0ac850" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetIncomeLoss_8fe2afae-fa83-4556-9a90-cea14eb5b08e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_NetIncomeLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_NetIncomeLoss_8fe2afae-fa83-4556-9a90-cea14eb5b08e" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EarningsPerShareBasic_0a0fda8c-437f-4bd8-a8fe-288f2d72e086" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EarningsPerShareBasic"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_EarningsPerShareBasic_0a0fda8c-437f-4bd8-a8fe-288f2d72e086" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EarningsPerShareDiluted_100904cb-b3b8-46ec-b5b4-9ebb3908ef6e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EarningsPerShareDiluted"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_EarningsPerShareDiluted_100904cb-b3b8-46ec-b5b4-9ebb3908ef6e" xlink:type="arc" order="9"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_WeightedAverageNumberOfSharesOutstandingBasic_7ee37780-8557-4bba-acd8-912b25dfe4b3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingBasic"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_WeightedAverageNumberOfSharesOutstandingBasic_7ee37780-8557-4bba-acd8-912b25dfe4b3" xlink:type="arc" order="10"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding_646a9e82-7fd1-4b5e-b9e4-31c79c3c19ec" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_6ad6809f-2f77-4576-90e3-f6108c5f957c" xlink:to="loc_us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding_646a9e82-7fd1-4b5e-b9e4-31c79c3c19ec" xlink:type="arc" order="11"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/ConsolidatedStatementsofOperationsParenthetical" xlink:type="simple" xlink:href="cdxs-20231231.xsd#ConsolidatedStatementsofOperationsParenthetical"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/ConsolidatedStatementsofOperationsParenthetical" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementLineItems_78db5001-679b-401b-83ed-673b105cce07" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementTable_2d794499-0d72-45b5-8029-a744bdc2595f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_StatementLineItems_78db5001-679b-401b-83ed-673b105cce07" xlink:to="loc_us-gaap_StatementTable_2d794499-0d72-45b5-8029-a744bdc2595f" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_155da834-9f42-4e58-9631-c9043f25c14b" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_2d794499-0d72-45b5-8029-a744bdc2595f" xlink:to="loc_srt_ProductOrServiceAxis_155da834-9f42-4e58-9631-c9043f25c14b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_155da834-9f42-4e58-9631-c9043f25c14b_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_155da834-9f42-4e58-9631-c9043f25c14b" xlink:to="loc_srt_ProductsAndServicesDomain_155da834-9f42-4e58-9631-c9043f25c14b_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_36f82efd-87b1-4730-b3d1-01a3d956e3a2" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_155da834-9f42-4e58-9631-c9043f25c14b" xlink:to="loc_srt_ProductsAndServicesDomain_36f82efd-87b1-4730-b3d1-01a3d956e3a2" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_94275bca-fe9a-4fa3-b1e8-89e6ef62e50c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_36f82efd-87b1-4730-b3d1-01a3d956e3a2" xlink:to="loc_us-gaap_ProductMember_94275bca-fe9a-4fa3-b1e8-89e6ef62e50c" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_63034f10-5028-4429-af51-808e3aa8e02d" xlink:href="cdxs-20231231.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_36f82efd-87b1-4730-b3d1-01a3d956e3a2" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_63034f10-5028-4429-af51-808e3aa8e02d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_e597cf2b-f73a-4b2b-aca3-d46658e18fdf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_2d794499-0d72-45b5-8029-a744bdc2595f" xlink:to="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_e597cf2b-f73a-4b2b-aca3-d46658e18fdf" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_e597cf2b-f73a-4b2b-aca3-d46658e18fdf_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_e597cf2b-f73a-4b2b-aca3-d46658e18fdf" xlink:to="loc_us-gaap_RelatedPartyDomain_e597cf2b-f73a-4b2b-aca3-d46658e18fdf_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_f98be929-c4a4-47eb-a337-aee637c156b4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_e597cf2b-f73a-4b2b-aca3-d46658e18fdf" xlink:to="loc_us-gaap_RelatedPartyDomain_f98be929-c4a4-47eb-a337-aee637c156b4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyMember_9370a742-821f-4a05-870f-b6e3bc26249e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyDomain_f98be929-c4a4-47eb-a337-aee637c156b4" xlink:to="loc_us-gaap_RelatedPartyMember_9370a742-821f-4a05-870f-b6e3bc26249e" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_4bb97918-13c4-4f95-a4d5-ebcb458d843c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_78db5001-679b-401b-83ed-673b105cce07" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_4bb97918-13c4-4f95-a4d5-ebcb458d843c" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherNonoperatingIncomeExpense_ff1b57e9-9eb8-46e2-b636-4bc32df33f5e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherNonoperatingIncomeExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_78db5001-679b-401b-83ed-673b105cce07" xlink:to="loc_us-gaap_OtherNonoperatingIncomeExpense_ff1b57e9-9eb8-46e2-b636-4bc32df33f5e" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/ConsolidatedStatementsofStockholdersEquity" xlink:type="simple" xlink:href="cdxs-20231231.xsd#ConsolidatedStatementsofStockholdersEquity"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/ConsolidatedStatementsofStockholdersEquity" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementLineItems_9a3651a1-d09a-4ccc-a5ce-394df3d3138b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementTable_b5b6fe56-a249-4af1-a06b-57f4f1e1bec1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_StatementLineItems_9a3651a1-d09a-4ccc-a5ce-394df3d3138b" xlink:to="loc_us-gaap_StatementTable_b5b6fe56-a249-4af1-a06b-57f4f1e1bec1" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementEquityComponentsAxis_aa075da3-a551-403b-9a4e-0ed2b484fc99" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementEquityComponentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_b5b6fe56-a249-4af1-a06b-57f4f1e1bec1" xlink:to="loc_us-gaap_StatementEquityComponentsAxis_aa075da3-a551-403b-9a4e-0ed2b484fc99" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquityComponentDomain_aa075da3-a551-403b-9a4e-0ed2b484fc99_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquityComponentDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementEquityComponentsAxis_aa075da3-a551-403b-9a4e-0ed2b484fc99" xlink:to="loc_us-gaap_EquityComponentDomain_aa075da3-a551-403b-9a4e-0ed2b484fc99_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquityComponentDomain_11afba08-a2d5-41d6-9f29-00eb25b93217" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquityComponentDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementEquityComponentsAxis_aa075da3-a551-403b-9a4e-0ed2b484fc99" xlink:to="loc_us-gaap_EquityComponentDomain_11afba08-a2d5-41d6-9f29-00eb25b93217" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockMember_ef4e8d1d-559f-4373-9273-f27d07aae121" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_11afba08-a2d5-41d6-9f29-00eb25b93217" xlink:to="loc_us-gaap_CommonStockMember_ef4e8d1d-559f-4373-9273-f27d07aae121" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AdditionalPaidInCapitalMember_cd71cd26-d8e7-4cda-8e94-38fd26731d17" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AdditionalPaidInCapitalMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_11afba08-a2d5-41d6-9f29-00eb25b93217" xlink:to="loc_us-gaap_AdditionalPaidInCapitalMember_cd71cd26-d8e7-4cda-8e94-38fd26731d17" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RetainedEarningsMember_a61db196-19c4-472f-bb34-c34f329d2848" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RetainedEarningsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_11afba08-a2d5-41d6-9f29-00eb25b93217" xlink:to="loc_us-gaap_RetainedEarningsMember_a61db196-19c4-472f-bb34-c34f329d2848" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusAxis_8aec48d9-6c32-4822-bbbe-7e679d5ca93f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_b5b6fe56-a249-4af1-a06b-57f4f1e1bec1" xlink:to="loc_us-gaap_GranteeStatusAxis_8aec48d9-6c32-4822-bbbe-7e679d5ca93f" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusDomain_8aec48d9-6c32-4822-bbbe-7e679d5ca93f_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_GranteeStatusAxis_8aec48d9-6c32-4822-bbbe-7e679d5ca93f" xlink:to="loc_us-gaap_GranteeStatusDomain_8aec48d9-6c32-4822-bbbe-7e679d5ca93f_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusDomain_0d644e87-1d98-4fc0-8e7e-f29bd39bc422" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_GranteeStatusAxis_8aec48d9-6c32-4822-bbbe-7e679d5ca93f" xlink:to="loc_us-gaap_GranteeStatusDomain_0d644e87-1d98-4fc0-8e7e-f29bd39bc422" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedPaymentArrangementEmployeeMember_4e7b9309-cee2-4330-8e09-03712e583a04" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedPaymentArrangementEmployeeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_GranteeStatusDomain_0d644e87-1d98-4fc0-8e7e-f29bd39bc422" xlink:to="loc_us-gaap_ShareBasedPaymentArrangementEmployeeMember_4e7b9309-cee2-4330-8e09-03712e583a04" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_7cf28fa4-bc17-401a-a6cd-d0c2dc1a15db" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedPaymentArrangementNonemployeeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_GranteeStatusDomain_0d644e87-1d98-4fc0-8e7e-f29bd39bc422" xlink:to="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_7cf28fa4-bc17-401a-a6cd-d0c2dc1a15db" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncreaseDecreaseInStockholdersEquityRollForward"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_9a3651a1-d09a-4ccc-a5ce-394df3d3138b" xlink:to="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharesOutstanding_9f7c6e6a-932b-444a-9087-e450b6c5e5ac" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharesOutstanding"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_SharesOutstanding_9f7c6e6a-932b-444a-9087-e450b6c5e5ac" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockholdersEquity_ead12e9a-0250-4c2c-8162-9f3aae3f7adf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockholdersEquity"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_StockholdersEquity_ead12e9a-0250-4c2c-8162-9f3aae3f7adf" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised_5b2a5bc5-ccd6-4ef0-9b0c-5b46b1e2a241" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised_5b2a5bc5-ccd6-4ef0-9b0c-5b46b1e2a241" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised_c1c06180-8104-49de-9613-e850d6b04f92" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised_c1c06180-8104-49de-9613-e850d6b04f92" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesOther_7d97afb7-0af7-459a-98d5-ef6b66e8ac0a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockIssuedDuringPeriodSharesOther"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesOther_7d97afb7-0af7-459a-98d5-ef6b66e8ac0a" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue_73df0175-350c-4ffd-a983-cd914dd9e1b6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue_73df0175-350c-4ffd-a983-cd914dd9e1b6" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharesPaidForTaxWithholdingForShareBasedCompensation_49f2ca9e-3664-4dd0-9daa-b94b1b0be1d7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharesPaidForTaxWithholdingForShareBasedCompensation"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_SharesPaidForTaxWithholdingForShareBasedCompensation_49f2ca9e-3664-4dd0-9daa-b94b1b0be1d7" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AdjustmentsRelatedToTaxWithholdingForShareBasedCompensation_dd6cbb40-b167-445e-aaad-6bd4cd8f2d0d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AdjustmentsRelatedToTaxWithholdingForShareBasedCompensation"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_AdjustmentsRelatedToTaxWithholdingForShareBasedCompensation_dd6cbb40-b167-445e-aaad-6bd4cd8f2d0d" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_ea89ac38-d7f2-4df9-b273-d359961a8960" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_ea89ac38-d7f2-4df9-b273-d359961a8960" xlink:type="arc" order="9"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodValueNewIssues_1dbda10b-b7ac-4cc4-93df-bdb95288e030" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockIssuedDuringPeriodValueNewIssues"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_StockIssuedDuringPeriodValueNewIssues_1dbda10b-b7ac-4cc4-93df-bdb95288e030" xlink:type="arc" order="10"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetIncomeLoss_52ba64ae-ea82-4d75-9c99-74251680b947" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_NetIncomeLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_a6828a53-73e6-47dd-8680-567461ce63c1" xlink:to="loc_us-gaap_NetIncomeLoss_52ba64ae-ea82-4d75-9c99-74251680b947" xlink:type="arc" order="11"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharesOutstanding_56d8f258-8b02-467d-b873-c46abddc93c2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharesOutstanding"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockholdersEquity_cddf0040-86e8-47a5-98cf-1ed128a56ac3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockholdersEquity"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/ConsolidatedStatementsofCashFlowsParenthetical" xlink:type="simple" xlink:href="cdxs-20231231.xsd#ConsolidatedStatementsofCashFlowsParenthetical"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/ConsolidatedStatementsofCashFlowsParenthetical" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementLineItems_3f156652-4df4-4f9b-81f7-b2639eb019d3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementTable_3097f772-6d93-423f-9964-f45d7adad1a6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_StatementLineItems_3f156652-4df4-4f9b-81f7-b2639eb019d3" xlink:to="loc_us-gaap_StatementTable_3097f772-6d93-423f-9964-f45d7adad1a6" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_4eabe8da-9d31-4cb2-a54d-c137d9e785e1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_3097f772-6d93-423f-9964-f45d7adad1a6" xlink:to="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_4eabe8da-9d31-4cb2-a54d-c137d9e785e1" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_4eabe8da-9d31-4cb2-a54d-c137d9e785e1_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_4eabe8da-9d31-4cb2-a54d-c137d9e785e1" xlink:to="loc_us-gaap_RelatedPartyDomain_4eabe8da-9d31-4cb2-a54d-c137d9e785e1_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_80b48d48-ebbb-47a1-a840-eaf89e091634" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_4eabe8da-9d31-4cb2-a54d-c137d9e785e1" xlink:to="loc_us-gaap_RelatedPartyDomain_80b48d48-ebbb-47a1-a840-eaf89e091634" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyMember_f746154a-1180-49df-947f-fb8323af9a36" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyDomain_80b48d48-ebbb-47a1-a840-eaf89e091634" xlink:to="loc_us-gaap_RelatedPartyMember_f746154a-1180-49df-947f-fb8323af9a36" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherNoncashIncome_3965f671-c137-4b09-a5ab-8d2a2ef65ead" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherNoncashIncome"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_3f156652-4df4-4f9b-81f7-b2639eb019d3" xlink:to="loc_us-gaap_OtherNoncashIncome_3965f671-c137-4b09-a5ab-8d2a2ef65ead" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesFvNiUnrealizedGainLoss_f9b1b119-d258-485d-9c5a-0791fac6d8bb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesFvNiUnrealizedGainLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_3f156652-4df4-4f9b-81f7-b2639eb019d3" xlink:to="loc_us-gaap_EquitySecuritiesFvNiUnrealizedGainLoss_f9b1b119-d258-485d-9c5a-0791fac6d8bb" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInContractWithCustomerLiability_94cc73d0-d70a-4fe7-a350-e36aa50b2b2d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncreaseDecreaseInContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_3f156652-4df4-4f9b-81f7-b2639eb019d3" xlink:to="loc_us-gaap_IncreaseDecreaseInContractWithCustomerLiability_94cc73d0-d70a-4fe7-a350-e36aa50b2b2d" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsToAcquireOtherInvestments_611bd455-43e3-4b02-ab69-739db18e6a2e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PaymentsToAcquireOtherInvestments"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_3f156652-4df4-4f9b-81f7-b2639eb019d3" xlink:to="loc_us-gaap_PaymentsToAcquireOtherInvestments_611bd455-43e3-4b02-ab69-739db18e6a2e" xlink:type="arc" order="3"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/BasisofPresentationandSummaryofSignificantAccountingPoliciesNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#BasisofPresentationandSummaryofSignificantAccountingPoliciesNarrativeDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/BasisofPresentationandSummaryofSignificantAccountingPoliciesNarrativeDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:href="cdxs-20231231.xsd#cdxs_AccountingPoliciesLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:href="cdxs-20231231.xsd#cdxs_AccountingPoliciesTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CreditFacilityAxis_cf0f0a5c-33dc-4c9f-8573-92dc4986f8f4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CreditFacilityAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:to="loc_us-gaap_CreditFacilityAxis_cf0f0a5c-33dc-4c9f-8573-92dc4986f8f4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CreditFacilityDomain_cf0f0a5c-33dc-4c9f-8573-92dc4986f8f4_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CreditFacilityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_CreditFacilityAxis_cf0f0a5c-33dc-4c9f-8573-92dc4986f8f4" xlink:to="loc_us-gaap_CreditFacilityDomain_cf0f0a5c-33dc-4c9f-8573-92dc4986f8f4_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CreditFacilityDomain_4358b1fe-6990-430d-b453-3b86ae2275ec" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CreditFacilityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_CreditFacilityAxis_cf0f0a5c-33dc-4c9f-8573-92dc4986f8f4" xlink:to="loc_us-gaap_CreditFacilityDomain_4358b1fe-6990-430d-b453-3b86ae2275ec" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LetterOfCreditMember_d84a407d-4bce-45cd-9c7e-ca7404ab2d84" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LetterOfCreditMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CreditFacilityDomain_4358b1fe-6990-430d-b453-3b86ae2275ec" xlink:to="loc_us-gaap_LetterOfCreditMember_d84a407d-4bce-45cd-9c7e-ca7404ab2d84" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_2a9347d5-af09-4dc7-833d-e9f65e0ebbaa" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_2a9347d5-af09-4dc7-833d-e9f65e0ebbaa" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_2a9347d5-af09-4dc7-833d-e9f65e0ebbaa_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_2a9347d5-af09-4dc7-833d-e9f65e0ebbaa" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_2a9347d5-af09-4dc7-833d-e9f65e0ebbaa_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_fa600db4-62d3-414c-a0dc-5367f002576f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_2a9347d5-af09-4dc7-833d-e9f65e0ebbaa" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_fa600db4-62d3-414c-a0dc-5367f002576f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CashDepositMember_89a160b8-35a8-4aac-b7ad-774554b036ce" xlink:href="cdxs-20231231.xsd#cdxs_CashDepositMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_fa600db4-62d3-414c-a0dc-5367f002576f" xlink:to="loc_cdxs_CashDepositMember_89a160b8-35a8-4aac-b7ad-774554b036ce" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_MajorCustomersAxis_cb4183f4-e1b9-4c93-b107-12cb8b96f6b1" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_MajorCustomersAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:to="loc_srt_MajorCustomersAxis_cb4183f4-e1b9-4c93-b107-12cb8b96f6b1" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_NameOfMajorCustomerDomain_cb4183f4-e1b9-4c93-b107-12cb8b96f6b1_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_NameOfMajorCustomerDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_MajorCustomersAxis_cb4183f4-e1b9-4c93-b107-12cb8b96f6b1" xlink:to="loc_srt_NameOfMajorCustomerDomain_cb4183f4-e1b9-4c93-b107-12cb8b96f6b1_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_NameOfMajorCustomerDomain_32702bf5-6833-4ef7-b0b1-ef6650d3adcc" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_NameOfMajorCustomerDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_MajorCustomersAxis_cb4183f4-e1b9-4c93-b107-12cb8b96f6b1" xlink:to="loc_srt_NameOfMajorCustomerDomain_32702bf5-6833-4ef7-b0b1-ef6650d3adcc" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_FourCustomersMember_cc2d4cfb-1622-4c0d-b382-371be2ed080e" xlink:href="cdxs-20231231.xsd#cdxs_FourCustomersMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_32702bf5-6833-4ef7-b0b1-ef6650d3adcc" xlink:to="loc_cdxs_FourCustomersMember_cc2d4cfb-1622-4c0d-b382-371be2ed080e" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TwoCustomersMember_75da6c66-f88f-4e1a-97fc-6e2da72259d3" xlink:href="cdxs-20231231.xsd#cdxs_TwoCustomersMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_32702bf5-6833-4ef7-b0b1-ef6650d3adcc" xlink:to="loc_cdxs_TwoCustomersMember_75da6c66-f88f-4e1a-97fc-6e2da72259d3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_b2e67791-af5f-4236-b01a-af03f230e794" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:to="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_b2e67791-af5f-4236-b01a-af03f230e794" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_b2e67791-af5f-4236-b01a-af03f230e794_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_b2e67791-af5f-4236-b01a-af03f230e794" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_b2e67791-af5f-4236-b01a-af03f230e794_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_f286ca5a-192f-487d-b5cc-e3898666cd64" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_b2e67791-af5f-4236-b01a-af03f230e794" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_f286ca5a-192f-487d-b5cc-e3898666cd64" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsReceivableMember_4b118a40-9bc4-4f57-bce4-2ec59d0310e2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AccountsReceivableMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_f286ca5a-192f-487d-b5cc-e3898666cd64" xlink:to="loc_us-gaap_AccountsReceivableMember_4b118a40-9bc4-4f57-bce4-2ec59d0310e2" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByTypeAxis_89ea3262-3b69-4b52-a99c-d05e17ec93ca" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:to="loc_us-gaap_ConcentrationRiskByTypeAxis_89ea3262-3b69-4b52-a99c-d05e17ec93ca" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_89ea3262-3b69-4b52-a99c-d05e17ec93ca_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_89ea3262-3b69-4b52-a99c-d05e17ec93ca" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_89ea3262-3b69-4b52-a99c-d05e17ec93ca_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_cd50fead-1a6c-4be2-aefe-ef16ee9b0406" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_89ea3262-3b69-4b52-a99c-d05e17ec93ca" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_cd50fead-1a6c-4be2-aefe-ef16ee9b0406" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CustomerConcentrationRiskMember_83a45484-d4b6-4ba4-80e7-0abaaf9100cd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CustomerConcentrationRiskMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskTypeDomain_cd50fead-1a6c-4be2-aefe-ef16ee9b0406" xlink:to="loc_us-gaap_CustomerConcentrationRiskMember_83a45484-d4b6-4ba4-80e7-0abaaf9100cd" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementBusinessSegmentsAxis_5822d4e2-5ced-45fc-8300-41180af1ef63" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementBusinessSegmentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_cdxs_AccountingPoliciesTable_676e7e8d-4012-43a5-9a33-c12330b0d4b4" xlink:to="loc_us-gaap_StatementBusinessSegmentsAxis_5822d4e2-5ced-45fc-8300-41180af1ef63" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SegmentDomain_5822d4e2-5ced-45fc-8300-41180af1ef63_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SegmentDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementBusinessSegmentsAxis_5822d4e2-5ced-45fc-8300-41180af1ef63" xlink:to="loc_us-gaap_SegmentDomain_5822d4e2-5ced-45fc-8300-41180af1ef63_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SegmentDomain_f232742c-514a-4d23-b116-2ec524f3b33e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SegmentDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementBusinessSegmentsAxis_5822d4e2-5ced-45fc-8300-41180af1ef63" xlink:to="loc_us-gaap_SegmentDomain_f232742c-514a-4d23-b116-2ec524f3b33e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_NovelBiotherapeuticsMember_7078f04e-623c-4c5f-8ebc-d31e3633c293" xlink:href="cdxs-20231231.xsd#cdxs_NovelBiotherapeuticsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SegmentDomain_f232742c-514a-4d23-b116-2ec524f3b33e" xlink:to="loc_cdxs_NovelBiotherapeuticsMember_7078f04e-623c-4c5f-8ebc-d31e3633c293" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShippingAndDistributionCost_f2fe995e-67fe-4e32-b886-1025d2838324" xlink:href="cdxs-20231231.xsd#cdxs_ShippingAndDistributionCost"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_cdxs_ShippingAndDistributionCost_f2fe995e-67fe-4e32-b886-1025d2838324" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AdvertisingExpense_191c8e37-5ebf-4f43-9a5a-4d7e80c01d80" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AdvertisingExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_us-gaap_AdvertisingExpense_191c8e37-5ebf-4f43-9a5a-4d7e80c01d80" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashCurrent_b7e7367c-6fef-403c-96f7-19c2cfe0219c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashCurrent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_us-gaap_RestrictedCashCurrent_b7e7367c-6fef-403c-96f7-19c2cfe0219c" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashNoncurrent_96356fce-b30c-4f57-83fe-09745355b368" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashNoncurrent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_us-gaap_RestrictedCashNoncurrent_96356fce-b30c-4f57-83fe-09745355b368" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskPercentage1_20f64ce9-1d90-4df8-8805-fae626b4fe49" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskPercentage1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_us-gaap_ConcentrationRiskPercentage1_20f64ce9-1d90-4df8-8805-fae626b4fe49" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ImpairmentOfLongLivedAssetsHeldForUse_877f8956-d899-4b28-ac6f-b74fbda746ee" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ImpairmentOfLongLivedAssetsHeldForUse"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_us-gaap_ImpairmentOfLongLivedAssetsHeldForUse_877f8956-d899-4b28-ac6f-b74fbda746ee" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_Goodwill_f399d95e-d412-4381-9b20-6dbcbf11148e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_Goodwill"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_us-gaap_Goodwill_f399d95e-d412-4381-9b20-6dbcbf11148e" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GoodwillImpairmentLoss_d5398cb4-3e01-4255-8b0b-0fb8d0e8ba36" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GoodwillImpairmentLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_AccountingPoliciesLineItems_d999eb8d-b1e5-4462-ab00-66ee25d4d7da" xlink:to="loc_us-gaap_GoodwillImpairmentLoss_d5398cb4-3e01-4255-8b0b-0fb8d0e8ba36" xlink:type="arc" order="7"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/BasisofPresentationandSummaryofSignificantAccountingPoliciesPropertyPlantandEquipmentDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#BasisofPresentationandSummaryofSignificantAccountingPoliciesPropertyPlantandEquipmentDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/BasisofPresentationandSummaryofSignificantAccountingPoliciesPropertyPlantandEquipmentDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentLineItems_7917d423-8597-41d3-a31f-487d5560a359" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_49e63ee7-fd71-4a03-8a38-e08cf62ab6db" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_7917d423-8597-41d3-a31f-487d5560a359" xlink:to="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_49e63ee7-fd71-4a03-8a38-e08cf62ab6db" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_3d7a1584-34ae-4da5-8b1b-8cd8bac35202" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_49e63ee7-fd71-4a03-8a38-e08cf62ab6db" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_3d7a1584-34ae-4da5-8b1b-8cd8bac35202" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_3d7a1584-34ae-4da5-8b1b-8cd8bac35202_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_3d7a1584-34ae-4da5-8b1b-8cd8bac35202" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_3d7a1584-34ae-4da5-8b1b-8cd8bac35202_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_97286535-9d84-44b1-938b-e4f617bcfbb7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_3d7a1584-34ae-4da5-8b1b-8cd8bac35202" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_97286535-9d84-44b1-938b-e4f617bcfbb7" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquipmentMember_ca2905c7-78a5-497d-b083-43f8509d43bd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquipmentMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_97286535-9d84-44b1-938b-e4f617bcfbb7" xlink:to="loc_us-gaap_EquipmentMember_ca2905c7-78a5-497d-b083-43f8509d43bd" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ComputerEquipmentAndSoftwareMember_1f1e725d-ecb7-42fe-b00d-acf0e1d0cea0" xlink:href="cdxs-20231231.xsd#cdxs_ComputerEquipmentAndSoftwareMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_97286535-9d84-44b1-938b-e4f617bcfbb7" xlink:to="loc_cdxs_ComputerEquipmentAndSoftwareMember_1f1e725d-ecb7-42fe-b00d-acf0e1d0cea0" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_OfficeEquipmentAndFurnitureMember_9de1efbe-0beb-45ef-8861-b3e4332d78fb" xlink:href="cdxs-20231231.xsd#cdxs_OfficeEquipmentAndFurnitureMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_97286535-9d84-44b1-938b-e4f617bcfbb7" xlink:to="loc_cdxs_OfficeEquipmentAndFurnitureMember_9de1efbe-0beb-45ef-8861-b3e4332d78fb" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentUsefulLife_838cfad1-71a4-4f3b-a17b-866dae68a88e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentUsefulLife"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_7917d423-8597-41d3-a31f-487d5560a359" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentUsefulLife_838cfad1-71a4-4f3b-a17b-866dae68a88e" xlink:type="arc" order="0"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/RevenueRecognitionDisaggregationofRevenueDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#RevenueRecognitionDisaggregationofRevenueDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/RevenueRecognitionDisaggregationofRevenueDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueLineItems_1292263d-418a-4699-a15f-81462c7dfc0b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueTable_f7d7bf95-5e10-46a3-b1fd-398eab19c1ee" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_1292263d-418a-4699-a15f-81462c7dfc0b" xlink:to="loc_us-gaap_DisaggregationOfRevenueTable_f7d7bf95-5e10-46a3-b1fd-398eab19c1ee" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_a13c67d7-da83-4256-8e1c-6c5c8357c906" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_f7d7bf95-5e10-46a3-b1fd-398eab19c1ee" xlink:to="loc_srt_ProductOrServiceAxis_a13c67d7-da83-4256-8e1c-6c5c8357c906" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_a13c67d7-da83-4256-8e1c-6c5c8357c906_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_a13c67d7-da83-4256-8e1c-6c5c8357c906" xlink:to="loc_srt_ProductsAndServicesDomain_a13c67d7-da83-4256-8e1c-6c5c8357c906_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_f0bef342-7755-4657-83fe-472098866a0d" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_a13c67d7-da83-4256-8e1c-6c5c8357c906" xlink:to="loc_srt_ProductsAndServicesDomain_f0bef342-7755-4657-83fe-472098866a0d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_f52a94ea-f20e-4b4b-a53b-ed2bb8e8a4a8" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_f0bef342-7755-4657-83fe-472098866a0d" xlink:to="loc_us-gaap_ProductMember_f52a94ea-f20e-4b4b-a53b-ed2bb8e8a4a8" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_3c3a2f6d-3c25-400e-9ee9-20715a739351" xlink:href="cdxs-20231231.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_f0bef342-7755-4657-83fe-472098866a0d" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_3c3a2f6d-3c25-400e-9ee9-20715a739351" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_StatementGeographicalAxis_3a444e9c-6ac8-4fc7-9460-99b5e8200ccf" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_StatementGeographicalAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_f7d7bf95-5e10-46a3-b1fd-398eab19c1ee" xlink:to="loc_srt_StatementGeographicalAxis_3a444e9c-6ac8-4fc7-9460-99b5e8200ccf" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_3a444e9c-6ac8-4fc7-9460-99b5e8200ccf_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_SegmentGeographicalDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_StatementGeographicalAxis_3a444e9c-6ac8-4fc7-9460-99b5e8200ccf" xlink:to="loc_srt_SegmentGeographicalDomain_3a444e9c-6ac8-4fc7-9460-99b5e8200ccf_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_2bc652a0-099b-4413-bc12-662b62b5e639" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_SegmentGeographicalDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_StatementGeographicalAxis_3a444e9c-6ac8-4fc7-9460-99b5e8200ccf" xlink:to="loc_srt_SegmentGeographicalDomain_2bc652a0-099b-4413-bc12-662b62b5e639" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_AmericasMember_037c6630-1cf2-400a-9c25-597fb4b89cc2" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_AmericasMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_2bc652a0-099b-4413-bc12-662b62b5e639" xlink:to="loc_srt_AmericasMember_037c6630-1cf2-400a-9c25-597fb4b89cc2" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EMEAMember_bea1f2e8-4b57-4180-9ec9-449d641feae3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EMEAMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_2bc652a0-099b-4413-bc12-662b62b5e639" xlink:to="loc_us-gaap_EMEAMember_bea1f2e8-4b57-4180-9ec9-449d641feae3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_AsiaPacificMember_6ae6c899-109c-46e8-9122-a3d34b7fb592" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_AsiaPacificMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_2bc652a0-099b-4413-bc12-662b62b5e639" xlink:to="loc_srt_AsiaPacificMember_6ae6c899-109c-46e8-9122-a3d34b7fb592" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_0a9a3630-c592-40a2-93da-859bf73a160e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_1292263d-418a-4699-a15f-81462c7dfc0b" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_0a9a3630-c592-40a2-93da-859bf73a160e" xlink:type="arc" order="0"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/RevenueRecognitionNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#RevenueRecognitionNarrativeDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/RevenueRecognitionNarrativeDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueLineItems_0c6bd635-9d21-42e1-afaa-ca8d5074b323" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueTable_4e8c5c36-ef44-4030-9daa-0a5dda7c1350" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_0c6bd635-9d21-42e1-afaa-ca8d5074b323" xlink:to="loc_us-gaap_DisaggregationOfRevenueTable_4e8c5c36-ef44-4030-9daa-0a5dda7c1350" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeAxis_c4174285-f56b-4c0a-86f2-19df81559adb" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_4e8c5c36-ef44-4030-9daa-0a5dda7c1350" xlink:to="loc_srt_RangeAxis_c4174285-f56b-4c0a-86f2-19df81559adb" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_c4174285-f56b-4c0a-86f2-19df81559adb_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_RangeAxis_c4174285-f56b-4c0a-86f2-19df81559adb" xlink:to="loc_srt_RangeMember_c4174285-f56b-4c0a-86f2-19df81559adb_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_cb460869-bcdc-4846-a0b2-1c4a8575d3d6" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_RangeAxis_c4174285-f56b-4c0a-86f2-19df81559adb" xlink:to="loc_srt_RangeMember_cb460869-bcdc-4846-a0b2-1c4a8575d3d6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_MinimumMember_8664d2ca-b119-44fc-b5cc-f4385b1cf78d" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_MinimumMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RangeMember_cb460869-bcdc-4846-a0b2-1c4a8575d3d6" xlink:to="loc_srt_MinimumMember_8664d2ca-b119-44fc-b5cc-f4385b1cf78d" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_MaximumMember_03704943-23e1-418c-b5e1-3f951ada5e57" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_MaximumMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RangeMember_cb460869-bcdc-4846-a0b2-1c4a8575d3d6" xlink:to="loc_srt_MaximumMember_03704943-23e1-418c-b5e1-3f951ada5e57" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_e772f90c-c57f-4438-84bd-1c4eb439f8ed" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_4e8c5c36-ef44-4030-9daa-0a5dda7c1350" xlink:to="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_e772f90c-c57f-4438-84bd-1c4eb439f8ed" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_e772f90c-c57f-4438-84bd-1c4eb439f8ed_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_e772f90c-c57f-4438-84bd-1c4eb439f8ed" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_e772f90c-c57f-4438-84bd-1c4eb439f8ed_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_6df483bb-7ade-4385-926f-c68fd5326180" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_e772f90c-c57f-4438-84bd-1c4eb439f8ed" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_6df483bb-7ade-4385-926f-c68fd5326180" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsReceivableMember_683f8d6e-3a9f-4dbc-8ae3-11ffa1c8e0dd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AccountsReceivableMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_6df483bb-7ade-4385-926f-c68fd5326180" xlink:to="loc_us-gaap_AccountsReceivableMember_683f8d6e-3a9f-4dbc-8ae3-11ffa1c8e0dd" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_487f3c89-80da-4842-ac96-19ec50cde15c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_4e8c5c36-ef44-4030-9daa-0a5dda7c1350" xlink:to="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_487f3c89-80da-4842-ac96-19ec50cde15c" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ReceivableTypeDomain_487f3c89-80da-4842-ac96-19ec50cde15c_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ReceivableTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_487f3c89-80da-4842-ac96-19ec50cde15c" xlink:to="loc_us-gaap_ReceivableTypeDomain_487f3c89-80da-4842-ac96-19ec50cde15c_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ReceivableTypeDomain_77ad7711-d24e-4d2b-b160-c12712318f68" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ReceivableTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_487f3c89-80da-4842-ac96-19ec50cde15c" xlink:to="loc_us-gaap_ReceivableTypeDomain_77ad7711-d24e-4d2b-b160-c12712318f68" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShortTermUnbilledReceivablesMember_b907c706-6518-4428-aa50-348153697e69" xlink:href="cdxs-20231231.xsd#cdxs_ShortTermUnbilledReceivablesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ReceivableTypeDomain_77ad7711-d24e-4d2b-b160-c12712318f68" xlink:to="loc_cdxs_ShortTermUnbilledReceivablesMember_b907c706-6518-4428-aa50-348153697e69" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_LongTermUnbilledReceivablesMember_c782e489-2b12-4b74-982c-46c721becffc" xlink:href="cdxs-20231231.xsd#cdxs_LongTermUnbilledReceivablesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ReceivableTypeDomain_77ad7711-d24e-4d2b-b160-c12712318f68" xlink:to="loc_cdxs_LongTermUnbilledReceivablesMember_c782e489-2b12-4b74-982c-46c721becffc" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueFromContractWithCustomerPaymentTerms_b0d1a532-bae8-430a-98ed-da13ed187157" xlink:href="cdxs-20231231.xsd#cdxs_RevenueFromContractWithCustomerPaymentTerms"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_0c6bd635-9d21-42e1-afaa-ca8d5074b323" xlink:to="loc_cdxs_RevenueFromContractWithCustomerPaymentTerms_b0d1a532-bae8-430a-98ed-da13ed187157" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_UnbilledReceivablesNotBillableAtBalanceSheetDate_c17e9872-6b89-4dc3-9011-9e41421d4979" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_UnbilledReceivablesNotBillableAtBalanceSheetDate"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_0c6bd635-9d21-42e1-afaa-ca8d5074b323" xlink:to="loc_us-gaap_UnbilledReceivablesNotBillableAtBalanceSheetDate_c17e9872-6b89-4dc3-9011-9e41421d4979" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerAssetCreditLossExpense_e9b14460-a278-495b-ad71-e271e81c0dbf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerAssetCreditLossExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_0c6bd635-9d21-42e1-afaa-ca8d5074b323" xlink:to="loc_us-gaap_ContractWithCustomerAssetCreditLossExpense_e9b14460-a278-495b-ad71-e271e81c0dbf" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/RevenueRecognitionPerformanceObligationDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#RevenueRecognitionPerformanceObligationDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/RevenueRecognitionPerformanceObligationDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueTable_20ed2f55-1f14-4067-b164-b9aba290562b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:to="loc_us-gaap_DisaggregationOfRevenueTable_20ed2f55-1f14-4067-b164-b9aba290562b" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_20ed2f55-1f14-4067-b164-b9aba290562b" xlink:to="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_86d803ab-7154-4147-85bb-34f8363fcb04_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:to="loc_srt_ProductsAndServicesDomain_86d803ab-7154-4147-85bb-34f8363fcb04_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_657988c5-77b4-4bfa-9e4d-d9974ad3fd81" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:to="loc_srt_ProductsAndServicesDomain_657988c5-77b4-4bfa-9e4d-d9974ad3fd81" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_69b7a004-5d82-4acc-98a0-2c2ddf1b5d98" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_657988c5-77b4-4bfa-9e4d-d9974ad3fd81" xlink:to="loc_us-gaap_ProductMember_69b7a004-5d82-4acc-98a0-2c2ddf1b5d98" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionStartDateAxis_92cf79dd-168d-411c-a7d6-7190f25a4c14" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionStartDateAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_20ed2f55-1f14-4067-b164-b9aba290562b" xlink:to="loc_us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionStartDateAxis_92cf79dd-168d-411c-a7d6-7190f25a4c14" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueRemainingPerformanceObligation_4395a8c9-a0fe-49bc-9523-01e1c20acbe6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueRemainingPerformanceObligation"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:to="loc_us-gaap_RevenueRemainingPerformanceObligation_4395a8c9-a0fe-49bc-9523-01e1c20acbe6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionPeriod1_ef9c4f0a-0b9b-4682-93c1-054fbcc3e58c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionPeriod1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:to="loc_us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionPeriod1_ef9c4f0a-0b9b-4682-93c1-054fbcc3e58c" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/RevenueRecognitionPerformanceObligationDetails_1" xlink:type="simple" xlink:href="cdxs-20231231.xsd#RevenueRecognitionPerformanceObligationDetails_1"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/RevenueRecognitionPerformanceObligationDetails_1" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueTable_20ed2f55-1f14-4067-b164-b9aba290562b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DisaggregationOfRevenueTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:to="loc_us-gaap_DisaggregationOfRevenueTable_20ed2f55-1f14-4067-b164-b9aba290562b" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_20ed2f55-1f14-4067-b164-b9aba290562b" xlink:to="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_86d803ab-7154-4147-85bb-34f8363fcb04_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:to="loc_srt_ProductsAndServicesDomain_86d803ab-7154-4147-85bb-34f8363fcb04_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_657988c5-77b4-4bfa-9e4d-d9974ad3fd81" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_86d803ab-7154-4147-85bb-34f8363fcb04" xlink:to="loc_srt_ProductsAndServicesDomain_657988c5-77b4-4bfa-9e4d-d9974ad3fd81" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_69b7a004-5d82-4acc-98a0-2c2ddf1b5d98" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_657988c5-77b4-4bfa-9e4d-d9974ad3fd81" xlink:to="loc_us-gaap_ProductMember_69b7a004-5d82-4acc-98a0-2c2ddf1b5d98" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueRemainingPerformanceObligation_4395a8c9-a0fe-49bc-9523-01e1c20acbe6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueRemainingPerformanceObligation"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:to="loc_us-gaap_RevenueRemainingPerformanceObligation_4395a8c9-a0fe-49bc-9523-01e1c20acbe6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionPeriod1_ef9c4f0a-0b9b-4682-93c1-054fbcc3e58c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionPeriod1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_921e6db7-20c9-4722-a887-fae507cc5d96" xlink:to="loc_us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionPeriod1_ef9c4f0a-0b9b-4682-93c1-054fbcc3e58c" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/NetLossperShareDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#NetLossperShareDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/NetLossperShareDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems_d8e4b5f4-2657-40f4-add9-3ef7a767df06" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable_a39afc55-fcb2-41a4-b69d-4ef9f94b7a2b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems_d8e4b5f4-2657-40f4-add9-3ef7a767df06" xlink:to="loc_us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable_a39afc55-fcb2-41a4-b69d-4ef9f94b7a2b" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_e4045f13-e01b-4415-973f-3506ceea6ddc" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable_a39afc55-fcb2-41a4-b69d-4ef9f94b7a2b" xlink:to="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_e4045f13-e01b-4415-973f-3506ceea6ddc" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesNameDomain_e4045f13-e01b-4415-973f-3506ceea6ddc_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AntidilutiveSecuritiesNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_e4045f13-e01b-4415-973f-3506ceea6ddc" xlink:to="loc_us-gaap_AntidilutiveSecuritiesNameDomain_e4045f13-e01b-4415-973f-3506ceea6ddc_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesNameDomain_64220323-1fbf-43db-9815-1e228d9fbc83" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AntidilutiveSecuritiesNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_e4045f13-e01b-4415-973f-3506ceea6ddc" xlink:to="loc_us-gaap_AntidilutiveSecuritiesNameDomain_64220323-1fbf-43db-9815-1e228d9fbc83" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockCompensationPlanMember_5472ff22-da9a-48be-85ce-c4816a5ae383" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockCompensationPlanMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_AntidilutiveSecuritiesNameDomain_64220323-1fbf-43db-9815-1e228d9fbc83" xlink:to="loc_us-gaap_StockCompensationPlanMember_5472ff22-da9a-48be-85ce-c4816a5ae383" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_6ce48a15-088f-4d39-8d4e-83b5486f21bc" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_AntidilutiveSecuritiesNameDomain_64220323-1fbf-43db-9815-1e228d9fbc83" xlink:to="loc_us-gaap_EmployeeStockMember_6ce48a15-088f-4d39-8d4e-83b5486f21bc" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount_0fc639c2-9237-4f68-8d02-d8423bc3a2ff" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems_d8e4b5f4-2657-40f4-add9-3ef7a767df06" xlink:to="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount_0fc639c2-9237-4f68-8d02-d8423bc3a2ff" xlink:type="arc" order="0"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsGSKPlatformTechnologyTransferCollaborationandLicenseAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsGSKPlatformTechnologyTransferCollaborationandLicenseAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsGSKPlatformTechnologyTransferCollaborationandLicenseAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8cb5ad7e-5ab8-45a6-8d84-aff862222a05" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_7a64a57a-7065-4f56-9867-122ae8b0db6b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8cb5ad7e-5ab8-45a6-8d84-aff862222a05" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_7a64a57a-7065-4f56-9867-122ae8b0db6b" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_0a496578-ec06-4169-8fa8-d267b5ae1afd" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_7a64a57a-7065-4f56-9867-122ae8b0db6b" xlink:to="loc_srt_CounterpartyNameAxis_0a496578-ec06-4169-8fa8-d267b5ae1afd" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_0a496578-ec06-4169-8fa8-d267b5ae1afd_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_0a496578-ec06-4169-8fa8-d267b5ae1afd" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_0a496578-ec06-4169-8fa8-d267b5ae1afd_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_80331232-b217-461d-afdc-e362c51dba2e" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_0a496578-ec06-4169-8fa8-d267b5ae1afd" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_80331232-b217-461d-afdc-e362c51dba2e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_GSKMember_988ff51a-1803-4aca-97f0-104046f406b7" xlink:href="cdxs-20231231.xsd#cdxs_GSKMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_80331232-b217-461d-afdc-e362c51dba2e" xlink:to="loc_cdxs_GSKMember_988ff51a-1803-4aca-97f0-104046f406b7" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeAxis_b932cf08-76fe-4a73-93d2-03def5b9dc70" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_7a64a57a-7065-4f56-9867-122ae8b0db6b" xlink:to="loc_srt_RangeAxis_b932cf08-76fe-4a73-93d2-03def5b9dc70" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_b932cf08-76fe-4a73-93d2-03def5b9dc70_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_RangeAxis_b932cf08-76fe-4a73-93d2-03def5b9dc70" xlink:to="loc_srt_RangeMember_b932cf08-76fe-4a73-93d2-03def5b9dc70_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_40fb81e8-d4ac-4b22-834e-238a0abbf3e7" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_RangeAxis_b932cf08-76fe-4a73-93d2-03def5b9dc70" xlink:to="loc_srt_RangeMember_40fb81e8-d4ac-4b22-834e-238a0abbf3e7" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_MinimumMember_7b203e27-3588-4f9a-baa0-fbe557eb7fb5" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_MinimumMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RangeMember_40fb81e8-d4ac-4b22-834e-238a0abbf3e7" xlink:to="loc_srt_MinimumMember_7b203e27-3588-4f9a-baa0-fbe557eb7fb5" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_MaximumMember_f4c04082-f1ac-4b0f-8b08-0b72a8e17064" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_MaximumMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RangeMember_40fb81e8-d4ac-4b22-834e-238a0abbf3e7" xlink:to="loc_srt_MaximumMember_f4c04082-f1ac-4b0f-8b08-0b72a8e17064" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_e3755ed4-8d11-451c-bd87-51293023a3aa" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_7a64a57a-7065-4f56-9867-122ae8b0db6b" xlink:to="loc_srt_ProductOrServiceAxis_e3755ed4-8d11-451c-bd87-51293023a3aa" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_e3755ed4-8d11-451c-bd87-51293023a3aa_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_e3755ed4-8d11-451c-bd87-51293023a3aa" xlink:to="loc_srt_ProductsAndServicesDomain_e3755ed4-8d11-451c-bd87-51293023a3aa_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_b104554b-17b7-40fc-94cc-3262fa4d73b7" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_e3755ed4-8d11-451c-bd87-51293023a3aa" xlink:to="loc_srt_ProductsAndServicesDomain_b104554b-17b7-40fc-94cc-3262fa4d73b7" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_d8a9a0a6-2192-4787-bc67-facdea473514" xlink:href="cdxs-20231231.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_b104554b-17b7-40fc-94cc-3262fa4d73b7" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_d8a9a0a6-2192-4787-bc67-facdea473514" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueFromCollaborativeArrangementContingentAmounts_9b9e2243-2b33-421f-bb9a-cf8d33ad9aff" xlink:href="cdxs-20231231.xsd#cdxs_RevenueFromCollaborativeArrangementContingentAmounts"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8cb5ad7e-5ab8-45a6-8d84-aff862222a05" xlink:to="loc_cdxs_RevenueFromCollaborativeArrangementContingentAmounts_9b9e2243-2b33-421f-bb9a-cf8d33ad9aff" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_b0ff48d9-8085-4a1a-992b-2ed320349e30" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8cb5ad7e-5ab8-45a6-8d84-aff862222a05" xlink:to="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_b0ff48d9-8085-4a1a-992b-2ed320349e30" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CollaborativeArrangementNumberOfMilestonePayments_0c476385-6dc4-4c37-bc0b-0c77385e6bc3" xlink:href="cdxs-20231231.xsd#cdxs_CollaborativeArrangementNumberOfMilestonePayments"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8cb5ad7e-5ab8-45a6-8d84-aff862222a05" xlink:to="loc_cdxs_CollaborativeArrangementNumberOfMilestonePayments_0c476385-6dc4-4c37-bc0b-0c77385e6bc3" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsMerckPlatformTechnologyTransferandLicenseAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsMerckPlatformTechnologyTransferandLicenseAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsMerckPlatformTechnologyTransferandLicenseAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_81fd92ac-14c2-431e-886b-8c656ece3768" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_9414c82b-9e69-4bb0-b5a1-ec59e830abdf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_81fd92ac-14c2-431e-886b-8c656ece3768" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_9414c82b-9e69-4bb0-b5a1-ec59e830abdf" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_cdfee816-e933-40d4-86e1-f8125d184d18" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_9414c82b-9e69-4bb0-b5a1-ec59e830abdf" xlink:to="loc_srt_CounterpartyNameAxis_cdfee816-e933-40d4-86e1-f8125d184d18" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_cdfee816-e933-40d4-86e1-f8125d184d18_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_cdfee816-e933-40d4-86e1-f8125d184d18" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_cdfee816-e933-40d4-86e1-f8125d184d18_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_f126f6f7-ac7e-4d4b-aa88-fa4a1bdfbf2e" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_cdfee816-e933-40d4-86e1-f8125d184d18" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_f126f6f7-ac7e-4d4b-aa88-fa4a1bdfbf2e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MerckMember_c7571b0c-b737-4884-895d-b845521794fb" xlink:href="cdxs-20231231.xsd#cdxs_MerckMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_f126f6f7-ac7e-4d4b-aa88-fa4a1bdfbf2e" xlink:to="loc_cdxs_MerckMember_c7571b0c-b737-4884-895d-b845521794fb" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfArrangementAxis_6172fdfc-5d4a-47ad-b7c8-75167b3392b3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfArrangementAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_9414c82b-9e69-4bb0-b5a1-ec59e830abdf" xlink:to="loc_us-gaap_TypeOfArrangementAxis_6172fdfc-5d4a-47ad-b7c8-75167b3392b3" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_6172fdfc-5d4a-47ad-b7c8-75167b3392b3_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_TypeOfArrangementAxis_6172fdfc-5d4a-47ad-b7c8-75167b3392b3" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_6172fdfc-5d4a-47ad-b7c8-75167b3392b3_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_f5bbebf0-a0bd-427f-a8e5-956cf854d964" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_TypeOfArrangementAxis_6172fdfc-5d4a-47ad-b7c8-75167b3392b3" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_f5bbebf0-a0bd-427f-a8e5-956cf854d964" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TechnologyTransferCollaborationandLicenseAgreementMember_af37eba0-178d-434e-838b-49a46c74aa21" xlink:href="cdxs-20231231.xsd#cdxs_TechnologyTransferCollaborationandLicenseAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_f5bbebf0-a0bd-427f-a8e5-956cf854d964" xlink:to="loc_cdxs_TechnologyTransferCollaborationandLicenseAgreementMember_af37eba0-178d-434e-838b-49a46c74aa21" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_206b7abf-d3ac-453b-8233-044238edb7d0" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_9414c82b-9e69-4bb0-b5a1-ec59e830abdf" xlink:to="loc_srt_ProductOrServiceAxis_206b7abf-d3ac-453b-8233-044238edb7d0" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_206b7abf-d3ac-453b-8233-044238edb7d0_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_206b7abf-d3ac-453b-8233-044238edb7d0" xlink:to="loc_srt_ProductsAndServicesDomain_206b7abf-d3ac-453b-8233-044238edb7d0_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_c6542330-7eba-40d6-9451-1eba99b37255" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_206b7abf-d3ac-453b-8233-044238edb7d0" xlink:to="loc_srt_ProductsAndServicesDomain_c6542330-7eba-40d6-9451-1eba99b37255" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_0b7e2fa9-01c6-4c1d-be4b-d6e44d966068" xlink:href="cdxs-20231231.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_c6542330-7eba-40d6-9451-1eba99b37255" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_0b7e2fa9-01c6-4c1d-be4b-d6e44d966068" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_4fb7db1f-6f1e-4c87-8edf-6f1cd0016290" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_81fd92ac-14c2-431e-886b-8c656ece3768" xlink:to="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_4fb7db1f-6f1e-4c87-8edf-6f1cd0016290" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentReceivable_9bda155b-32d9-4c8a-93b8-5d24828cf653" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentReceivable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_81fd92ac-14c2-431e-886b-8c656ece3768" xlink:to="loc_cdxs_RevenueRecognitionContingentReceivable_9bda155b-32d9-4c8a-93b8-5d24828cf653" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsMerckSitagliptinCatalystSupplyAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsMerckSitagliptinCatalystSupplyAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsMerckSitagliptinCatalystSupplyAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_e8c0e3bd-648c-4367-9550-f45f49401595" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_3d42e55c-d5de-4ae9-9eac-f9ad94ba7a6e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_e8c0e3bd-648c-4367-9550-f45f49401595" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_3d42e55c-d5de-4ae9-9eac-f9ad94ba7a6e" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_2e64a2a2-dd27-4a0a-ade7-06c5f3cfc7c9" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_3d42e55c-d5de-4ae9-9eac-f9ad94ba7a6e" xlink:to="loc_srt_CounterpartyNameAxis_2e64a2a2-dd27-4a0a-ade7-06c5f3cfc7c9" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_2e64a2a2-dd27-4a0a-ade7-06c5f3cfc7c9_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_2e64a2a2-dd27-4a0a-ade7-06c5f3cfc7c9" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_2e64a2a2-dd27-4a0a-ade7-06c5f3cfc7c9_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_74090cb1-eb8b-42c8-ad49-7e8bc76ac5b5" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_2e64a2a2-dd27-4a0a-ade7-06c5f3cfc7c9" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_74090cb1-eb8b-42c8-ad49-7e8bc76ac5b5" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MerckMember_abbc2b95-edd0-4787-a305-e32d77213471" xlink:href="cdxs-20231231.xsd#cdxs_MerckMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_74090cb1-eb8b-42c8-ad49-7e8bc76ac5b5" xlink:to="loc_cdxs_MerckMember_abbc2b95-edd0-4787-a305-e32d77213471" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfArrangementAxis_a190f3db-b3d2-421e-b360-352455397f9d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfArrangementAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_3d42e55c-d5de-4ae9-9eac-f9ad94ba7a6e" xlink:to="loc_us-gaap_TypeOfArrangementAxis_a190f3db-b3d2-421e-b360-352455397f9d" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_a190f3db-b3d2-421e-b360-352455397f9d_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_TypeOfArrangementAxis_a190f3db-b3d2-421e-b360-352455397f9d" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_a190f3db-b3d2-421e-b360-352455397f9d_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_d361bdc3-09fc-4bdc-ad67-12a2ef27c440" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_TypeOfArrangementAxis_a190f3db-b3d2-421e-b360-352455397f9d" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_d361bdc3-09fc-4bdc-ad67-12a2ef27c440" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SupplyAgreementMember_e69e3980-4da7-4c14-b4c1-c198552f4ba4" xlink:href="cdxs-20231231.xsd#cdxs_SupplyAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_d361bdc3-09fc-4bdc-ad67-12a2ef27c440" xlink:to="loc_cdxs_SupplyAgreementMember_e69e3980-4da7-4c14-b4c1-c198552f4ba4" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_79ecdf29-13c5-4d49-8e6d-a68c8a87a00a" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_3d42e55c-d5de-4ae9-9eac-f9ad94ba7a6e" xlink:to="loc_srt_ProductOrServiceAxis_79ecdf29-13c5-4d49-8e6d-a68c8a87a00a" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_79ecdf29-13c5-4d49-8e6d-a68c8a87a00a_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_79ecdf29-13c5-4d49-8e6d-a68c8a87a00a" xlink:to="loc_srt_ProductsAndServicesDomain_79ecdf29-13c5-4d49-8e6d-a68c8a87a00a_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_6f660d29-792a-45d4-a754-e11c67594be6" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_79ecdf29-13c5-4d49-8e6d-a68c8a87a00a" xlink:to="loc_srt_ProductsAndServicesDomain_6f660d29-792a-45d4-a754-e11c67594be6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_2f3aebfa-4fd9-40b2-b021-252a9c6b2039" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_6f660d29-792a-45d4-a754-e11c67594be6" xlink:to="loc_us-gaap_ProductMember_2f3aebfa-4fd9-40b2-b021-252a9c6b2039" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SitagliptinEnzymeMember_e40f9e0b-d932-4c40-b211-98fc8f5f1956" xlink:href="cdxs-20231231.xsd#cdxs_SitagliptinEnzymeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_6f660d29-792a-45d4-a754-e11c67594be6" xlink:to="loc_cdxs_SitagliptinEnzymeMember_e40f9e0b-d932-4c40-b211-98fc8f5f1956" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_ab18abd5-ed25-4ee2-bf68-89526761fd5a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_3d42e55c-d5de-4ae9-9eac-f9ad94ba7a6e" xlink:to="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_ab18abd5-ed25-4ee2-bf68-89526761fd5a" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_ab18abd5-ed25-4ee2-bf68-89526761fd5a_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_ab18abd5-ed25-4ee2-bf68-89526761fd5a" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_ab18abd5-ed25-4ee2-bf68-89526761fd5a_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_41be4801-faee-4956-b3e6-5e6e79f0dfb6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_ab18abd5-ed25-4ee2-bf68-89526761fd5a" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_41be4801-faee-4956-b3e6-5e6e79f0dfb6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SalesRevenueNetMember_36ea0bc7-07bd-4847-bad1-6ff3af7e0bf2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SalesRevenueNetMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_41be4801-faee-4956-b3e6-5e6e79f0dfb6" xlink:to="loc_us-gaap_SalesRevenueNetMember_36ea0bc7-07bd-4847-bad1-6ff3af7e0bf2" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByTypeAxis_c61dc869-4db7-47b3-b9b1-08e350f37a77" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_3d42e55c-d5de-4ae9-9eac-f9ad94ba7a6e" xlink:to="loc_us-gaap_ConcentrationRiskByTypeAxis_c61dc869-4db7-47b3-b9b1-08e350f37a77" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_c61dc869-4db7-47b3-b9b1-08e350f37a77_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_c61dc869-4db7-47b3-b9b1-08e350f37a77" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_c61dc869-4db7-47b3-b9b1-08e350f37a77_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_87e580a6-35ac-4efd-b63f-334fe95093f3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_c61dc869-4db7-47b3-b9b1-08e350f37a77" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_87e580a6-35ac-4efd-b63f-334fe95093f3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CollaborativeArrangementConcentrationRiskMember_86ccbcfe-39c3-449a-a14e-e11214303907" xlink:href="cdxs-20231231.xsd#cdxs_CollaborativeArrangementConcentrationRiskMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskTypeDomain_87e580a6-35ac-4efd-b63f-334fe95093f3" xlink:to="loc_cdxs_CollaborativeArrangementConcentrationRiskMember_86ccbcfe-39c3-449a-a14e-e11214303907" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TermOfCollaborativeResearchAndDevelopmentAgreement_d5ee0882-47d5-44cb-8111-e9d365eab8c6" xlink:href="cdxs-20231231.xsd#cdxs_TermOfCollaborativeResearchAndDevelopmentAgreement"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_e8c0e3bd-648c-4367-9550-f45f49401595" xlink:to="loc_cdxs_TermOfCollaborativeResearchAndDevelopmentAgreement_d5ee0882-47d5-44cb-8111-e9d365eab8c6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_e3e84c7e-3616-4a83-8eae-d1cf57e373f2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_e8c0e3bd-648c-4367-9550-f45f49401595" xlink:to="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_e3e84c7e-3616-4a83-8eae-d1cf57e373f2" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskPercentage1_1922b6b7-7aa0-476b-b0f1-ded71dc3189f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskPercentage1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_e8c0e3bd-648c-4367-9550-f45f49401595" xlink:to="loc_us-gaap_ConcentrationRiskPercentage1_1922b6b7-7aa0-476b-b0f1-ded71dc3189f" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_a2bb48c7-8192-4855-8c13-2af776ed61c0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_e8c0e3bd-648c-4367-9550-f45f49401595" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_a2bb48c7-8192-4855-8c13-2af776ed61c0" xlink:type="arc" order="3"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsEnzymeSupplyAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsEnzymeSupplyAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsEnzymeSupplyAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d10e590-4f8a-4e50-b500-22c401800aed" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_ddb74f17-7f29-4f74-8f63-4f4c924faec3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d10e590-4f8a-4e50-b500-22c401800aed" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_ddb74f17-7f29-4f74-8f63-4f4c924faec3" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_bfb30864-fd23-4a1f-9249-b791925a12ec" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_ddb74f17-7f29-4f74-8f63-4f4c924faec3" xlink:to="loc_srt_ProductOrServiceAxis_bfb30864-fd23-4a1f-9249-b791925a12ec" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_bfb30864-fd23-4a1f-9249-b791925a12ec_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_bfb30864-fd23-4a1f-9249-b791925a12ec" xlink:to="loc_srt_ProductsAndServicesDomain_bfb30864-fd23-4a1f-9249-b791925a12ec_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_df7a6243-d998-4d89-b6ab-0adee63e779e" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_bfb30864-fd23-4a1f-9249-b791925a12ec" xlink:to="loc_srt_ProductsAndServicesDomain_df7a6243-d998-4d89-b6ab-0adee63e779e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_8d91edbc-13d7-4cfa-a183-c155b7097652" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_df7a6243-d998-4d89-b6ab-0adee63e779e" xlink:to="loc_us-gaap_ProductMember_8d91edbc-13d7-4cfa-a183-c155b7097652" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfArrangementAxis_8830253c-1c1b-4af6-8343-3d521c581714" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfArrangementAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_ddb74f17-7f29-4f74-8f63-4f4c924faec3" xlink:to="loc_us-gaap_TypeOfArrangementAxis_8830253c-1c1b-4af6-8343-3d521c581714" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_8830253c-1c1b-4af6-8343-3d521c581714_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_TypeOfArrangementAxis_8830253c-1c1b-4af6-8343-3d521c581714" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_8830253c-1c1b-4af6-8343-3d521c581714_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_35426c9a-2a75-40ad-b7f9-465c527a1d20" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_TypeOfArrangementAxis_8830253c-1c1b-4af6-8343-3d521c581714" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_35426c9a-2a75-40ad-b7f9-465c527a1d20" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_EnzymeSupplyAgreementMember_7ca063be-3a38-482b-8a98-48001111e0a6" xlink:href="cdxs-20231231.xsd#cdxs_EnzymeSupplyAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_35426c9a-2a75-40ad-b7f9-465c527a1d20" xlink:to="loc_cdxs_EnzymeSupplyAgreementMember_7ca063be-3a38-482b-8a98-48001111e0a6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SupplyAgreementMember_d6e22c03-e1c3-4612-9fd1-11c2b3c4ddd8" xlink:href="cdxs-20231231.xsd#cdxs_SupplyAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_35426c9a-2a75-40ad-b7f9-465c527a1d20" xlink:to="loc_cdxs_SupplyAgreementMember_d6e22c03-e1c3-4612-9fd1-11c2b3c4ddd8" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_704d18d0-25bc-4a1c-a5c1-a11460bf09ac" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d10e590-4f8a-4e50-b500-22c401800aed" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_704d18d0-25bc-4a1c-a5c1-a11460bf09ac" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueFromContractWithCustomerSettlementFee_e93cc65d-7fdb-419d-9e69-23d9904e57b6" xlink:href="cdxs-20231231.xsd#cdxs_RevenueFromContractWithCustomerSettlementFee"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d10e590-4f8a-4e50-b500-22c401800aed" xlink:to="loc_cdxs_RevenueFromContractWithCustomerSettlementFee_e93cc65d-7fdb-419d-9e69-23d9904e57b6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiability_ecf40123-b175-4210-a5d8-0d1c48b8f32a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d10e590-4f8a-4e50-b500-22c401800aed" xlink:to="loc_us-gaap_ContractWithCustomerLiability_ecf40123-b175-4210-a5d8-0d1c48b8f32a" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsCommercialAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsCommercialAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsCommercialAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d5e07cd-31b2-4ec3-8ed6-194d246606b9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a36e5a44-2e6a-4b49-956c-d5c92250b92e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d5e07cd-31b2-4ec3-8ed6-194d246606b9" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a36e5a44-2e6a-4b49-956c-d5c92250b92e" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_1d0d34b4-851e-4721-ae6f-3320b802903a" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a36e5a44-2e6a-4b49-956c-d5c92250b92e" xlink:to="loc_srt_CounterpartyNameAxis_1d0d34b4-851e-4721-ae6f-3320b802903a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_1d0d34b4-851e-4721-ae6f-3320b802903a_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_1d0d34b4-851e-4721-ae6f-3320b802903a" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_1d0d34b4-851e-4721-ae6f-3320b802903a_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_079b33fa-055f-4364-9a5a-7e4f87cd49d5" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_1d0d34b4-851e-4721-ae6f-3320b802903a" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_079b33fa-055f-4364-9a5a-7e4f87cd49d5" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TateLyleMember_ea013bfc-9ad4-4092-b805-ee342f8a2217" xlink:href="cdxs-20231231.xsd#cdxs_TateLyleMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_079b33fa-055f-4364-9a5a-7e4f87cd49d5" xlink:to="loc_cdxs_TateLyleMember_ea013bfc-9ad4-4092-b805-ee342f8a2217" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfArrangementAxis_dbb23e87-ce7a-422e-99ef-4ed25d02cf32" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfArrangementAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a36e5a44-2e6a-4b49-956c-d5c92250b92e" xlink:to="loc_us-gaap_TypeOfArrangementAxis_dbb23e87-ce7a-422e-99ef-4ed25d02cf32" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_dbb23e87-ce7a-422e-99ef-4ed25d02cf32_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_TypeOfArrangementAxis_dbb23e87-ce7a-422e-99ef-4ed25d02cf32" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_dbb23e87-ce7a-422e-99ef-4ed25d02cf32_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_564428c8-3fec-426d-a4c9-abe2cdb49232" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_TypeOfArrangementAxis_dbb23e87-ce7a-422e-99ef-4ed25d02cf32" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_564428c8-3fec-426d-a4c9-abe2cdb49232" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CommercialAgreementMember_1880573a-a89f-4656-817b-5c9733fe0152" xlink:href="cdxs-20231231.xsd#cdxs_CommercialAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_564428c8-3fec-426d-a4c9-abe2cdb49232" xlink:to="loc_cdxs_CommercialAgreementMember_1880573a-a89f-4656-817b-5c9733fe0152" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentReceivable_d60662ec-9d12-4edf-a1cb-3aef1e0fef99" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentReceivable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d5e07cd-31b2-4ec3-8ed6-194d246606b9" xlink:to="loc_cdxs_RevenueRecognitionContingentReceivable_d60662ec-9d12-4edf-a1cb-3aef1e0fef99" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ReceivableFromCollaborativeArrangement_83f6e6ec-b8dc-4756-84d1-ea664389d8e6" xlink:href="cdxs-20231231.xsd#cdxs_ReceivableFromCollaborativeArrangement"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_0d5e07cd-31b2-4ec3-8ed6-194d246606b9" xlink:to="loc_cdxs_ReceivableFromCollaborativeArrangement_83f6e6ec-b8dc-4756-84d1-ea664389d8e6" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsGlobalDevelopmentOptionandLicenseAgreementandStrategicCollaborationAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsGlobalDevelopmentOptionandLicenseAgreementandStrategicCollaborationAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsGlobalDevelopmentOptionandLicenseAgreementandStrategicCollaborationAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_5cebb18c-9d03-4655-88a3-b8e3706ff99c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a954a0b1-615e-4f04-9f11-c358adadb1c3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_5cebb18c-9d03-4655-88a3-b8e3706ff99c" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a954a0b1-615e-4f04-9f11-c358adadb1c3" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_ea8b3833-58e4-4711-9fc0-b15a58a473c4" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a954a0b1-615e-4f04-9f11-c358adadb1c3" xlink:to="loc_srt_CounterpartyNameAxis_ea8b3833-58e4-4711-9fc0-b15a58a473c4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_ea8b3833-58e4-4711-9fc0-b15a58a473c4_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_ea8b3833-58e4-4711-9fc0-b15a58a473c4" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_ea8b3833-58e4-4711-9fc0-b15a58a473c4_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_65d65b02-cd44-4758-88a0-f6227065fa54" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_ea8b3833-58e4-4711-9fc0-b15a58a473c4" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_65d65b02-cd44-4758-88a0-f6227065fa54" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_NestecLtd.NestleHealthSciencesMember_5cbec396-3fe0-42ee-a3e6-49b3587d2575" xlink:href="cdxs-20231231.xsd#cdxs_NestecLtd.NestleHealthSciencesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_65d65b02-cd44-4758-88a0-f6227065fa54" xlink:to="loc_cdxs_NestecLtd.NestleHealthSciencesMember_5cbec396-3fe0-42ee-a3e6-49b3587d2575" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfArrangementAxis_1ddc78f0-2fce-4cc8-ad82-4cc1589c032a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfArrangementAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_a954a0b1-615e-4f04-9f11-c358adadb1c3" xlink:to="loc_us-gaap_TypeOfArrangementAxis_1ddc78f0-2fce-4cc8-ad82-4cc1589c032a" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_1ddc78f0-2fce-4cc8-ad82-4cc1589c032a_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_TypeOfArrangementAxis_1ddc78f0-2fce-4cc8-ad82-4cc1589c032a" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_1ddc78f0-2fce-4cc8-ad82-4cc1589c032a_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_c9b117b2-6645-4427-ab8f-2bea401a067c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_TypeOfArrangementAxis_1ddc78f0-2fce-4cc8-ad82-4cc1589c032a" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_c9b117b2-6645-4427-ab8f-2bea401a067c" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_StrategicCollaborationAgreementMember_bf9390d3-2ce8-4b39-b0e8-123434c07857" xlink:href="cdxs-20231231.xsd#cdxs_StrategicCollaborationAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_c9b117b2-6645-4427-ab8f-2bea401a067c" xlink:to="loc_cdxs_StrategicCollaborationAgreementMember_bf9390d3-2ce8-4b39-b0e8-123434c07857" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_aa1a3d5e-b9ef-4d43-94a1-5af8a252bc5a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_5cebb18c-9d03-4655-88a3-b8e3706ff99c" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_aa1a3d5e-b9ef-4d43-94a1-5af8a252bc5a" xlink:type="arc" order="0"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsAcquisitionAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsAcquisitionAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsAcquisitionAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8622bb6f-84ac-4115-9088-b84d56baaca8" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_43796676-e05b-4760-b499-6a0dde3608a0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8622bb6f-84ac-4115-9088-b84d56baaca8" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_43796676-e05b-4760-b499-6a0dde3608a0" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_969fa8fa-3242-449d-bb93-4926ea040924" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_43796676-e05b-4760-b499-6a0dde3608a0" xlink:to="loc_srt_CounterpartyNameAxis_969fa8fa-3242-449d-bb93-4926ea040924" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_969fa8fa-3242-449d-bb93-4926ea040924_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_969fa8fa-3242-449d-bb93-4926ea040924" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_969fa8fa-3242-449d-bb93-4926ea040924_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_e76b854d-03a7-492d-86a6-384ded7e9e91" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_969fa8fa-3242-449d-bb93-4926ea040924" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_e76b854d-03a7-492d-86a6-384ded7e9e91" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_NestleHealthScienceMember_dd5b6c48-5202-4c29-ba54-eac27ab5839b" xlink:href="cdxs-20231231.xsd#cdxs_NestleHealthScienceMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_e76b854d-03a7-492d-86a6-384ded7e9e91" xlink:to="loc_cdxs_NestleHealthScienceMember_dd5b6c48-5202-4c29-ba54-eac27ab5839b" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfArrangementAxis_6df80cde-eae6-4750-bba9-b48a177ee2f0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfArrangementAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_43796676-e05b-4760-b499-6a0dde3608a0" xlink:to="loc_us-gaap_TypeOfArrangementAxis_6df80cde-eae6-4750-bba9-b48a177ee2f0" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_6df80cde-eae6-4750-bba9-b48a177ee2f0_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_TypeOfArrangementAxis_6df80cde-eae6-4750-bba9-b48a177ee2f0" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_6df80cde-eae6-4750-bba9-b48a177ee2f0_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_bb6906ba-1fb3-4b3e-a74c-c7b15e3b356b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_TypeOfArrangementAxis_6df80cde-eae6-4750-bba9-b48a177ee2f0" xlink:to="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_bb6906ba-1fb3-4b3e-a74c-c7b15e3b356b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_AcquisitionAgreementMember_c50c9c5b-ae94-4096-ac27-5a305f084117" xlink:href="cdxs-20231231.xsd#cdxs_AcquisitionAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ArrangementsAndNonarrangementTransactionsMember_bb6906ba-1fb3-4b3e-a74c-c7b15e3b356b" xlink:to="loc_cdxs_AcquisitionAgreementMember_c50c9c5b-ae94-4096-ac27-5a305f084117" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeAxis_6e1be2b5-e8d8-45b9-ac46-2778df6eb13b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_43796676-e05b-4760-b499-6a0dde3608a0" xlink:to="loc_us-gaap_SubsequentEventTypeAxis_6e1be2b5-e8d8-45b9-ac46-2778df6eb13b" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_6e1be2b5-e8d8-45b9-ac46-2778df6eb13b_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_6e1be2b5-e8d8-45b9-ac46-2778df6eb13b" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_6e1be2b5-e8d8-45b9-ac46-2778df6eb13b_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_58754407-3a4b-4475-bc91-c0377c773960" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_6e1be2b5-e8d8-45b9-ac46-2778df6eb13b" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_58754407-3a4b-4475-bc91-c0377c773960" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventMember_791e4cf5-2ea4-43a7-af2d-5959bb672182" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventTypeDomain_58754407-3a4b-4475-bc91-c0377c773960" xlink:to="loc_us-gaap_SubsequentEventMember_791e4cf5-2ea4-43a7-af2d-5959bb672182" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_725c300a-f72c-434c-8717-1d854ed78258" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8622bb6f-84ac-4115-9088-b84d56baaca8" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_725c300a-f72c-434c-8717-1d854ed78258" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CollaborativeArrangementUpfrontFeeAmount_bdcee3fa-ea0e-4e8a-a8d9-643b1fd2b174" xlink:href="cdxs-20231231.xsd#cdxs_CollaborativeArrangementUpfrontFeeAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_8622bb6f-84ac-4115-9088-b84d56baaca8" xlink:to="loc_cdxs_CollaborativeArrangementUpfrontFeeAmount_bdcee3fa-ea0e-4e8a-a8d9-643b1fd2b174" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsStrategicCollaborationAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsStrategicCollaborationAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsStrategicCollaborationAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_233f03c8-3c0b-4957-bc10-ccb706c6133f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_c9c478ef-a091-413b-9f86-346d6c5ea2f6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_233f03c8-3c0b-4957-bc10-ccb706c6133f" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_c9c478ef-a091-413b-9f86-346d6c5ea2f6" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_3d7f5429-3bde-4590-b92d-32cbcde5ceab" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_c9c478ef-a091-413b-9f86-346d6c5ea2f6" xlink:to="loc_srt_CounterpartyNameAxis_3d7f5429-3bde-4590-b92d-32cbcde5ceab" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_3d7f5429-3bde-4590-b92d-32cbcde5ceab_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_3d7f5429-3bde-4590-b92d-32cbcde5ceab" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_3d7f5429-3bde-4590-b92d-32cbcde5ceab_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_ade630e2-c5cb-4747-bb4d-294214ef36ca" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_3d7f5429-3bde-4590-b92d-32cbcde5ceab" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_ade630e2-c5cb-4747-bb4d-294214ef36ca" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PortonMember_da057bcf-9228-42c2-b152-9b1b16f2448d" xlink:href="cdxs-20231231.xsd#cdxs_PortonMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_ade630e2-c5cb-4747-bb4d-294214ef36ca" xlink:to="loc_cdxs_PortonMember_da057bcf-9228-42c2-b152-9b1b16f2448d" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_45579b66-1bad-4686-8f43-7d8ee6c1ac93" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_c9c478ef-a091-413b-9f86-346d6c5ea2f6" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_45579b66-1bad-4686-8f43-7d8ee6c1ac93" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_45579b66-1bad-4686-8f43-7d8ee6c1ac93_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_45579b66-1bad-4686-8f43-7d8ee6c1ac93" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_45579b66-1bad-4686-8f43-7d8ee6c1ac93_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_f2d6f9e2-4054-4c8e-aa9f-de313b22babd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_45579b66-1bad-4686-8f43-7d8ee6c1ac93" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_f2d6f9e2-4054-4c8e-aa9f-de313b22babd" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MilestoneOneMember_d7caf4ff-a52c-4013-a51d-cc1604be1c92" xlink:href="cdxs-20231231.xsd#cdxs_MilestoneOneMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_f2d6f9e2-4054-4c8e-aa9f-de313b22babd" xlink:to="loc_cdxs_MilestoneOneMember_d7caf4ff-a52c-4013-a51d-cc1604be1c92" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MilestoneTwoMember_c5f370af-fe43-46b9-b8a7-3cf2107be8b3" xlink:href="cdxs-20231231.xsd#cdxs_MilestoneTwoMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_f2d6f9e2-4054-4c8e-aa9f-de313b22babd" xlink:to="loc_cdxs_MilestoneTwoMember_c5f370af-fe43-46b9-b8a7-3cf2107be8b3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiability_9ef07e30-8d48-429b-8170-1369c6e3900c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_233f03c8-3c0b-4957-bc10-ccb706c6133f" xlink:to="loc_us-gaap_ContractWithCustomerLiability_9ef07e30-8d48-429b-8170-1369c6e3900c" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentReceivable_ccb97a6a-c81e-4550-9f24-a1e16d3bf479" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentReceivable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_233f03c8-3c0b-4957-bc10-ccb706c6133f" xlink:to="loc_cdxs_RevenueRecognitionContingentReceivable_ccb97a6a-c81e-4550-9f24-a1e16d3bf479" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionMilestoneRevenueNumberOfDaysForPayment_87a386bf-7220-4398-963f-41a9f6f059a0" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionMilestoneRevenueNumberOfDaysForPayment"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_233f03c8-3c0b-4957-bc10-ccb706c6133f" xlink:to="loc_cdxs_RevenueRecognitionMilestoneRevenueNumberOfDaysForPayment_87a386bf-7220-4398-963f-41a9f6f059a0" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProceedsFromCollaborators_54f12eb9-d113-4a87-8d63-65881210340a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProceedsFromCollaborators"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_233f03c8-3c0b-4957-bc10-ccb706c6133f" xlink:to="loc_us-gaap_ProceedsFromCollaborators_54f12eb9-d113-4a87-8d63-65881210340a" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_b2e54c37-f705-4360-a880-edc358c1221b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_233f03c8-3c0b-4957-bc10-ccb706c6133f" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_b2e54c37-f705-4360-a880-edc358c1221b" xlink:type="arc" order="4"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsPlatformTechnologyTransferandLicenseAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsPlatformTechnologyTransferandLicenseAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsPlatformTechnologyTransferandLicenseAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_39a96b6b-4a72-486b-a60a-6fe93c0ba520" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_39a96b6b-4a72-486b-a60a-6fe93c0ba520" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_74b611fd-24d7-4985-a6a8-a3b6b1e33496" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_39a96b6b-4a72-486b-a60a-6fe93c0ba520" xlink:to="loc_srt_CounterpartyNameAxis_74b611fd-24d7-4985-a6a8-a3b6b1e33496" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_74b611fd-24d7-4985-a6a8-a3b6b1e33496_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_74b611fd-24d7-4985-a6a8-a3b6b1e33496" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_74b611fd-24d7-4985-a6a8-a3b6b1e33496_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_162e291e-1084-40c2-9e5a-d6e2a79968db" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_74b611fd-24d7-4985-a6a8-a3b6b1e33496" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_162e291e-1084-40c2-9e5a-d6e2a79968db" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_NovartisMember_a9aa5600-87af-4d8d-a166-13d716ec222a" xlink:href="cdxs-20231231.xsd#cdxs_NovartisMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_162e291e-1084-40c2-9e5a-d6e2a79968db" xlink:to="loc_cdxs_NovartisMember_a9aa5600-87af-4d8d-a166-13d716ec222a" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_d50c2189-4956-4250-90ff-19f31812df75" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_39a96b6b-4a72-486b-a60a-6fe93c0ba520" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_d50c2189-4956-4250-90ff-19f31812df75" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_d50c2189-4956-4250-90ff-19f31812df75_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_d50c2189-4956-4250-90ff-19f31812df75" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_d50c2189-4956-4250-90ff-19f31812df75_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_2b52a4a0-08a9-4376-83da-ca2503860069" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_d50c2189-4956-4250-90ff-19f31812df75" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_2b52a4a0-08a9-4376-83da-ca2503860069" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MilestoneOneMember_ce84f54d-9264-4c32-b8bb-83ca8415e33a" xlink:href="cdxs-20231231.xsd#cdxs_MilestoneOneMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_2b52a4a0-08a9-4376-83da-ca2503860069" xlink:to="loc_cdxs_MilestoneOneMember_ce84f54d-9264-4c32-b8bb-83ca8415e33a" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MilestoneTwoMember_2008134f-88e8-4418-873e-d5834e62b26e" xlink:href="cdxs-20231231.xsd#cdxs_MilestoneTwoMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_2b52a4a0-08a9-4376-83da-ca2503860069" xlink:to="loc_cdxs_MilestoneTwoMember_2008134f-88e8-4418-873e-d5834e62b26e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_48f6544a-2de4-4a79-8728-f658a1d5eb1c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_39a96b6b-4a72-486b-a60a-6fe93c0ba520" xlink:to="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_48f6544a-2de4-4a79-8728-f658a1d5eb1c" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_48f6544a-2de4-4a79-8728-f658a1d5eb1c_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_48f6544a-2de4-4a79-8728-f658a1d5eb1c" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_48f6544a-2de4-4a79-8728-f658a1d5eb1c_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_4ae645f9-8b20-4f45-8049-288a94823784" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_48f6544a-2de4-4a79-8728-f658a1d5eb1c" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_4ae645f9-8b20-4f45-8049-288a94823784" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ComputerEquipmentAndSoftwareMember_4313dae1-179c-4124-9929-4a0b398343a6" xlink:href="cdxs-20231231.xsd#cdxs_ComputerEquipmentAndSoftwareMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_4ae645f9-8b20-4f45-8049-288a94823784" xlink:to="loc_cdxs_ComputerEquipmentAndSoftwareMember_4313dae1-179c-4124-9929-4a0b398343a6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiability_c2e64dfc-ee13-4c89-9757-597691fa1018" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_us-gaap_ContractWithCustomerLiability_c2e64dfc-ee13-4c89-9757-597691fa1018" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentReceivable_2411c41c-d87f-4e4f-b8bf-bd049c21d0b0" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentReceivable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_cdxs_RevenueRecognitionContingentReceivable_2411c41c-d87f-4e4f-b8bf-bd049c21d0b0" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentAnnualPaymentsTerm_dbbcd376-671a-4da1-b101-ca3ec138eb09" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentAnnualPaymentsTerm"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_cdxs_RevenueRecognitionContingentAnnualPaymentsTerm_dbbcd376-671a-4da1-b101-ca3ec138eb09" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentAnnualReceivableIncrease_4aeac44f-0bc7-45dc-89cf-60a890764895" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentAnnualReceivableIncrease"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_cdxs_RevenueRecognitionContingentAnnualReceivableIncrease_4aeac44f-0bc7-45dc-89cf-60a890764895" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionAnnualPayment_f15242c3-3f86-4090-9055-e18599d02c93" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionAnnualPayment"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_cdxs_RevenueRecognitionAnnualPayment_f15242c3-3f86-4090-9055-e18599d02c93" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionNumberOfAnnualPayment_4043c422-fe62-429a-84bf-985896eab5b2" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionNumberOfAnnualPayment"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_cdxs_RevenueRecognitionNumberOfAnnualPayment_4043c422-fe62-429a-84bf-985896eab5b2" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_a56da70c-d297-465a-b6b5-6e931a28aeda" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_f83f1882-ebfe-4554-bbc9-2bc622b34311" xlink:to="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_a56da70c-d297-465a-b6b5-6e931a28aeda" xlink:type="arc" order="6"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsLicenseAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsLicenseAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsLicenseAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_05cffe9e-d4e9-4b4d-9de7-41f3b127a9ef" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_01a5fac5-3f0e-48e3-a58f-f555dafcf0d9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_05cffe9e-d4e9-4b4d-9de7-41f3b127a9ef" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_01a5fac5-3f0e-48e3-a58f-f555dafcf0d9" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_4fa847d6-acb0-4353-80e5-46204e06da9c" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_01a5fac5-3f0e-48e3-a58f-f555dafcf0d9" xlink:to="loc_srt_CounterpartyNameAxis_4fa847d6-acb0-4353-80e5-46204e06da9c" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_4fa847d6-acb0-4353-80e5-46204e06da9c_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_4fa847d6-acb0-4353-80e5-46204e06da9c" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_4fa847d6-acb0-4353-80e5-46204e06da9c_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_e1033964-c6d8-4186-bcf8-b8d280e3d2ef" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_4fa847d6-acb0-4353-80e5-46204e06da9c" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_e1033964-c6d8-4186-bcf8-b8d280e3d2ef" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RocheMember_a0fe292e-e9c0-4db0-bf0b-9caafb5a7e93" xlink:href="cdxs-20231231.xsd#cdxs_RocheMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_e1033964-c6d8-4186-bcf8-b8d280e3d2ef" xlink:to="loc_cdxs_RocheMember_a0fe292e-e9c0-4db0-bf0b-9caafb5a7e93" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_5041da26-6240-494c-8994-1182a90b1641" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_01a5fac5-3f0e-48e3-a58f-f555dafcf0d9" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_5041da26-6240-494c-8994-1182a90b1641" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_5041da26-6240-494c-8994-1182a90b1641_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_5041da26-6240-494c-8994-1182a90b1641" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_5041da26-6240-494c-8994-1182a90b1641_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_482b016f-b4f9-4a9f-99a7-2858aa57e08f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_5041da26-6240-494c-8994-1182a90b1641" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_482b016f-b4f9-4a9f-99a7-2858aa57e08f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MilestoneOneMember_85669a75-6632-4401-949a-7fd5fda119e7" xlink:href="cdxs-20231231.xsd#cdxs_MilestoneOneMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_482b016f-b4f9-4a9f-99a7-2858aa57e08f" xlink:to="loc_cdxs_MilestoneOneMember_85669a75-6632-4401-949a-7fd5fda119e7" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MilestoneTwoMember_53aff73f-a799-410f-9783-3bceb9a6f8b4" xlink:href="cdxs-20231231.xsd#cdxs_MilestoneTwoMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_482b016f-b4f9-4a9f-99a7-2858aa57e08f" xlink:to="loc_cdxs_MilestoneTwoMember_53aff73f-a799-410f-9783-3bceb9a6f8b4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeAxis_59c53dbd-da69-499c-b8c7-7cfce972a4be" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_01a5fac5-3f0e-48e3-a58f-f555dafcf0d9" xlink:to="loc_us-gaap_SubsequentEventTypeAxis_59c53dbd-da69-499c-b8c7-7cfce972a4be" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_59c53dbd-da69-499c-b8c7-7cfce972a4be_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_59c53dbd-da69-499c-b8c7-7cfce972a4be" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_59c53dbd-da69-499c-b8c7-7cfce972a4be_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_12faacee-a4f6-4d2a-9ddf-fe3ef9675ecf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_59c53dbd-da69-499c-b8c7-7cfce972a4be" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_12faacee-a4f6-4d2a-9ddf-fe3ef9675ecf" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventMember_a4a0fc6c-35dc-43bd-88c0-382b6f7c8fe3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventTypeDomain_12faacee-a4f6-4d2a-9ddf-fe3ef9675ecf" xlink:to="loc_us-gaap_SubsequentEventMember_a4a0fc6c-35dc-43bd-88c0-382b6f7c8fe3" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiability_70ebde3d-6d91-4d5c-9bb0-bc2e24915fc5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_05cffe9e-d4e9-4b4d-9de7-41f3b127a9ef" xlink:to="loc_us-gaap_ContractWithCustomerLiability_70ebde3d-6d91-4d5c-9bb0-bc2e24915fc5" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionMilestoneRevenueNumberOfDaysForPayment_63238704-a1cb-4c1d-a6df-548b6bf257b8" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionMilestoneRevenueNumberOfDaysForPayment"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_05cffe9e-d4e9-4b4d-9de7-41f3b127a9ef" xlink:to="loc_cdxs_RevenueRecognitionMilestoneRevenueNumberOfDaysForPayment_63238704-a1cb-4c1d-a6df-548b6bf257b8" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentReceivable_3327d405-01da-4aac-b9ea-eb5fb73118b9" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentReceivable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_05cffe9e-d4e9-4b4d-9de7-41f3b127a9ef" xlink:to="loc_cdxs_RevenueRecognitionContingentReceivable_3327d405-01da-4aac-b9ea-eb5fb73118b9" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_09a246ac-c994-4054-adb6-8776ac544f3b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_05cffe9e-d4e9-4b4d-9de7-41f3b127a9ef" xlink:to="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_09a246ac-c994-4054-adb6-8776ac544f3b" xlink:type="arc" order="3"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsStrategicCollaborationandLicenseAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsStrategicCollaborationandLicenseAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsStrategicCollaborationandLicenseAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_9745bb9b-953a-4a61-8b9b-de211a98e7a0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_0410bb58-9bea-4603-aafb-5ddf924b612a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_9745bb9b-953a-4a61-8b9b-de211a98e7a0" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_0410bb58-9bea-4603-aafb-5ddf924b612a" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_c35f2782-e8a3-4203-9ace-7fd7cd578a0b" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_0410bb58-9bea-4603-aafb-5ddf924b612a" xlink:to="loc_srt_CounterpartyNameAxis_c35f2782-e8a3-4203-9ace-7fd7cd578a0b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_c35f2782-e8a3-4203-9ace-7fd7cd578a0b_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_c35f2782-e8a3-4203-9ace-7fd7cd578a0b" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_c35f2782-e8a3-4203-9ace-7fd7cd578a0b_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_7b2a5eb5-1c41-4937-b554-5fc1a5b2a8d4" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_c35f2782-e8a3-4203-9ace-7fd7cd578a0b" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_7b2a5eb5-1c41-4937-b554-5fc1a5b2a8d4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TakedaPharmaceuticalCoLtdMember_cbd48bee-e80b-43f4-acf1-b92168ef0538" xlink:href="cdxs-20231231.xsd#cdxs_TakedaPharmaceuticalCoLtdMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_7b2a5eb5-1c41-4937-b554-5fc1a5b2a8d4" xlink:to="loc_cdxs_TakedaPharmaceuticalCoLtdMember_cbd48bee-e80b-43f4-acf1-b92168ef0538" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_8ee14392-4aca-4ad3-aa06-a7330bdc1768" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_0410bb58-9bea-4603-aafb-5ddf924b612a" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_8ee14392-4aca-4ad3-aa06-a7330bdc1768" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_8ee14392-4aca-4ad3-aa06-a7330bdc1768_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_8ee14392-4aca-4ad3-aa06-a7330bdc1768" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_8ee14392-4aca-4ad3-aa06-a7330bdc1768_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_279cc0ff-6bb5-4655-b48d-f06ae6c6769b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersByTypeAxis_8ee14392-4aca-4ad3-aa06-a7330bdc1768" xlink:to="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_279cc0ff-6bb5-4655-b48d-f06ae6c6769b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_UpFrontPaymentMember_f04b29f3-16a7-45b2-901e-cceb1e00a71e" xlink:href="cdxs-20231231.xsd#cdxs_UpFrontPaymentMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_279cc0ff-6bb5-4655-b48d-f06ae6c6769b" xlink:to="loc_cdxs_UpFrontPaymentMember_f04b29f3-16a7-45b2-901e-cceb1e00a71e" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MilestonePaymentPerTargetGeneMember_21ab048d-0ab1-4a93-a907-a2d42854a5b9" xlink:href="cdxs-20231231.xsd#cdxs_MilestonePaymentPerTargetGeneMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ResearchAndDevelopmentArrangementContractToPerformForOthersTypeDomain_279cc0ff-6bb5-4655-b48d-f06ae6c6769b" xlink:to="loc_cdxs_MilestonePaymentPerTargetGeneMember_21ab048d-0ab1-4a93-a907-a2d42854a5b9" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiability_8c810a70-750a-44d5-aeff-a3834dbdc1d0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_9745bb9b-953a-4a61-8b9b-de211a98e7a0" xlink:to="loc_us-gaap_ContractWithCustomerLiability_8c810a70-750a-44d5-aeff-a3834dbdc1d0" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RevenueRecognitionContingentReceivable_e7ed1693-8511-49c3-bdbd-fcac575c6c74" xlink:href="cdxs-20231231.xsd#cdxs_RevenueRecognitionContingentReceivable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_9745bb9b-953a-4a61-8b9b-de211a98e7a0" xlink:to="loc_cdxs_RevenueRecognitionContingentReceivable_e7ed1693-8511-49c3-bdbd-fcac575c6c74" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ContractWithCustomerLiabilityRevenueRecognizedIncludingOpeningBalance_b49ea6c8-c232-4ed0-9863-df38d14b6eda" xlink:href="cdxs-20231231.xsd#cdxs_ContractWithCustomerLiabilityRevenueRecognizedIncludingOpeningBalance"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_9745bb9b-953a-4a61-8b9b-de211a98e7a0" xlink:to="loc_cdxs_ContractWithCustomerLiabilityRevenueRecognizedIncludingOpeningBalance_b49ea6c8-c232-4ed0-9863-df38d14b6eda" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsMasterCollaborationandResearchAgreementStockPurchaseAgreementandEnzymeSupplyAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsMasterCollaborationandResearchAgreementStockPurchaseAgreementandEnzymeSupplyAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsMasterCollaborationandResearchAgreementStockPurchaseAgreementandEnzymeSupplyAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_b1c39ea1-ea71-42ee-9434-3625bf8a291b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_b1c39ea1-ea71-42ee-9434-3625bf8a291b" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_7031b13f-b6f1-4de3-aca0-18e21b4ddbe4" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_b1c39ea1-ea71-42ee-9434-3625bf8a291b" xlink:to="loc_srt_CounterpartyNameAxis_7031b13f-b6f1-4de3-aca0-18e21b4ddbe4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_7031b13f-b6f1-4de3-aca0-18e21b4ddbe4_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_7031b13f-b6f1-4de3-aca0-18e21b4ddbe4" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_7031b13f-b6f1-4de3-aca0-18e21b4ddbe4_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_37ac4931-1e45-42c6-ab45-f14607d64471" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_7031b13f-b6f1-4de3-aca0-18e21b4ddbe4" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_37ac4931-1e45-42c6-ab45-f14607d64471" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MolecularAssembliesIncMember_0c631ea0-6984-4b94-885b-70f0a3eb3fb5" xlink:href="cdxs-20231231.xsd#cdxs_MolecularAssembliesIncMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_37ac4931-1e45-42c6-ab45-f14607d64471" xlink:to="loc_cdxs_MolecularAssembliesIncMember_0c631ea0-6984-4b94-885b-70f0a3eb3fb5" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MAIAgreementMember_03437d44-c982-4bed-978f-677d7720b9e8" xlink:href="cdxs-20231231.xsd#cdxs_MAIAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_37ac4931-1e45-42c6-ab45-f14607d64471" xlink:to="loc_cdxs_MAIAgreementMember_03437d44-c982-4bed-978f-677d7720b9e8" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementClassOfStockAxis_7e24418b-6b2c-4af7-a571-b111257587c3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementClassOfStockAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_b1c39ea1-ea71-42ee-9434-3625bf8a291b" xlink:to="loc_us-gaap_StatementClassOfStockAxis_7e24418b-6b2c-4af7-a571-b111257587c3" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_7e24418b-6b2c-4af7-a571-b111257587c3_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementClassOfStockAxis_7e24418b-6b2c-4af7-a571-b111257587c3" xlink:to="loc_us-gaap_ClassOfStockDomain_7e24418b-6b2c-4af7-a571-b111257587c3_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_e2299ae2-a646-42c3-b8ef-b17e1ddac9a2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementClassOfStockAxis_7e24418b-6b2c-4af7-a571-b111257587c3" xlink:to="loc_us-gaap_ClassOfStockDomain_e2299ae2-a646-42c3-b8ef-b17e1ddac9a2" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SeriesAPreferredStockMember_7c3867df-b27e-4c83-aebb-8d4bcda9ed18" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SeriesAPreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_e2299ae2-a646-42c3-b8ef-b17e1ddac9a2" xlink:to="loc_us-gaap_SeriesAPreferredStockMember_7c3867df-b27e-4c83-aebb-8d4bcda9ed18" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SeriesBPreferredStockMember_56147251-c94d-4be5-80d7-ce559c62bb3a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SeriesBPreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_e2299ae2-a646-42c3-b8ef-b17e1ddac9a2" xlink:to="loc_us-gaap_SeriesBPreferredStockMember_56147251-c94d-4be5-80d7-ce559c62bb3a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeriesAAndBPreferredStockMember_ef38689e-12ee-4291-b342-079c6979752e" xlink:href="cdxs-20231231.xsd#cdxs_SeriesAAndBPreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_e2299ae2-a646-42c3-b8ef-b17e1ddac9a2" xlink:to="loc_cdxs_SeriesAAndBPreferredStockMember_ef38689e-12ee-4291-b342-079c6979752e" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_39939df6-2c0b-4637-996e-ca71c59392fc" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_b1c39ea1-ea71-42ee-9434-3625bf8a291b" xlink:to="loc_srt_ProductOrServiceAxis_39939df6-2c0b-4637-996e-ca71c59392fc" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_39939df6-2c0b-4637-996e-ca71c59392fc_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_39939df6-2c0b-4637-996e-ca71c59392fc" xlink:to="loc_srt_ProductsAndServicesDomain_39939df6-2c0b-4637-996e-ca71c59392fc_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_1196c7a9-bbab-4555-aabc-bebd62449faf" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_39939df6-2c0b-4637-996e-ca71c59392fc" xlink:to="loc_srt_ProductsAndServicesDomain_1196c7a9-bbab-4555-aabc-bebd62449faf" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RoyaltyMember_2fc8dcca-8178-43d5-8812-a28a95169253" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RoyaltyMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_1196c7a9-bbab-4555-aabc-bebd62449faf" xlink:to="loc_us-gaap_RoyaltyMember_2fc8dcca-8178-43d5-8812-a28a95169253" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_a306a5a4-9b78-4d2f-8534-9b9f6b6dd94d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_1196c7a9-bbab-4555-aabc-bebd62449faf" xlink:to="loc_us-gaap_ProductMember_a306a5a4-9b78-4d2f-8534-9b9f6b6dd94d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionAxis_df189b4d-d2fe-4c6a-915d-b0e4515f346e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_b1c39ea1-ea71-42ee-9434-3625bf8a291b" xlink:to="loc_us-gaap_RelatedPartyTransactionAxis_df189b4d-d2fe-4c6a-915d-b0e4515f346e" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionDomain_df189b4d-d2fe-4c6a-915d-b0e4515f346e_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RelatedPartyTransactionAxis_df189b4d-d2fe-4c6a-915d-b0e4515f346e" xlink:to="loc_us-gaap_RelatedPartyTransactionDomain_df189b4d-d2fe-4c6a-915d-b0e4515f346e_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionDomain_7258c4fe-0e00-4fd0-8173-11738e7f6e30" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RelatedPartyTransactionAxis_df189b4d-d2fe-4c6a-915d-b0e4515f346e" xlink:to="loc_us-gaap_RelatedPartyTransactionDomain_7258c4fe-0e00-4fd0-8173-11738e7f6e30" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CommercializationAndEnzymeSupplyAgreementMember_02fb85a3-5b0c-469b-ab55-548084ee116b" xlink:href="cdxs-20231231.xsd#cdxs_CommercializationAndEnzymeSupplyAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyTransactionDomain_7258c4fe-0e00-4fd0-8173-11738e7f6e30" xlink:to="loc_cdxs_CommercializationAndEnzymeSupplyAgreementMember_02fb85a3-5b0c-469b-ab55-548084ee116b" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MasterCollaborationResearchAgreementMember_2c4f2cca-09e6-4d27-965a-9f54868723d6" xlink:href="cdxs-20231231.xsd#cdxs_MasterCollaborationResearchAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyTransactionDomain_7258c4fe-0e00-4fd0-8173-11738e7f6e30" xlink:to="loc_cdxs_MasterCollaborationResearchAgreementMember_2c4f2cca-09e6-4d27-965a-9f54868723d6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_cc4b623d-314c-479c-8cac-1faa2e5337f4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_b1c39ea1-ea71-42ee-9434-3625bf8a291b" xlink:to="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_cc4b623d-314c-479c-8cac-1faa2e5337f4" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_cc4b623d-314c-479c-8cac-1faa2e5337f4_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_cc4b623d-314c-479c-8cac-1faa2e5337f4" xlink:to="loc_us-gaap_RelatedPartyDomain_cc4b623d-314c-479c-8cac-1faa2e5337f4_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_020f8e33-64d4-49c9-95aa-bab4ffed3eeb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_cc4b623d-314c-479c-8cac-1faa2e5337f4" xlink:to="loc_us-gaap_RelatedPartyDomain_020f8e33-64d4-49c9-95aa-bab4ffed3eeb" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyMember_dec91eb4-5008-419a-a93f-e869f43a734a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyDomain_020f8e33-64d4-49c9-95aa-bab4ffed3eeb" xlink:to="loc_us-gaap_RelatedPartyMember_dec91eb4-5008-419a-a93f-e869f43a734a" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentOwnedBalanceShares_85609ea0-4456-4425-985d-be59f89a1e1c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_InvestmentOwnedBalanceShares"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_us-gaap_InvestmentOwnedBalanceShares_85609ea0-4456-4425-985d-be59f89a1e1c" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsToAcquireOtherInvestments_9f168552-5d81-4918-8ba7-8a8037fb4808" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PaymentsToAcquireOtherInvestments"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_us-gaap_PaymentsToAcquireOtherInvestments_9f168552-5d81-4918-8ba7-8a8037fb4808" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiability_ef5d0e63-9ee4-44f3-9725-a29ecfa8c4f6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_us-gaap_ContractWithCustomerLiability_ef5d0e63-9ee4-44f3-9725-a29ecfa8c4f6" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ContractWithCustomerSalesMilestone_eb0d1bfd-07db-4030-a9ba-57a0de8afec2" xlink:href="cdxs-20231231.xsd#cdxs_ContractWithCustomerSalesMilestone"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_cdxs_ContractWithCustomerSalesMilestone_eb0d1bfd-07db-4030-a9ba-57a0de8afec2" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RelatedPartyTransactionMilestonePaymentReceived_a5fa7eed-ca61-46a4-beed-a061e1546c8c" xlink:href="cdxs-20231231.xsd#cdxs_RelatedPartyTransactionMilestonePaymentReceived"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_cdxs_RelatedPartyTransactionMilestonePaymentReceived_a5fa7eed-ca61-46a4-beed-a061e1546c8c" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueSharesMilestonePaymentsReceived_ee0ec62a-b6db-46b2-9c79-4fd02f61f0c0" xlink:href="cdxs-20231231.xsd#cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueSharesMilestonePaymentsReceived"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueSharesMilestonePaymentsReceived_ee0ec62a-b6db-46b2-9c79-4fd02f61f0c0" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_NonmonetaryTransactionGrossOperatingRevenueRecognized_a10bee6b-dd7f-45af-b20b-76a4734aeb56" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_NonmonetaryTransactionGrossOperatingRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3d58876e-0297-42a5-8811-cccffd8b29e0" xlink:to="loc_us-gaap_NonmonetaryTransactionGrossOperatingRevenueRecognized_a10bee6b-dd7f-45af-b20b-76a4734aeb56" xlink:type="arc" order="6"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CollaborativeArrangementsPfizerEnzymeSupplyAgreementDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CollaborativeArrangementsPfizerEnzymeSupplyAgreementDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CollaborativeArrangementsPfizerEnzymeSupplyAgreementDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_1d598e71-37ab-4a56-8dfc-f70fd01e9e72" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_1d598e71-37ab-4a56-8dfc-f70fd01e9e72" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_944f6cb7-3ce0-49c3-a08d-4daaf1cd28a9" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_1d598e71-37ab-4a56-8dfc-f70fd01e9e72" xlink:to="loc_srt_CounterpartyNameAxis_944f6cb7-3ce0-49c3-a08d-4daaf1cd28a9" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_944f6cb7-3ce0-49c3-a08d-4daaf1cd28a9_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_944f6cb7-3ce0-49c3-a08d-4daaf1cd28a9" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_944f6cb7-3ce0-49c3-a08d-4daaf1cd28a9_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_c0ccda59-62be-4d19-8365-a42ab9a9042a" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_944f6cb7-3ce0-49c3-a08d-4daaf1cd28a9" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_c0ccda59-62be-4d19-8365-a42ab9a9042a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PfizerMember_ea7255d8-3e9f-44ce-8f03-11cb20890746" xlink:href="cdxs-20231231.xsd#cdxs_PfizerMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_c0ccda59-62be-4d19-8365-a42ab9a9042a" xlink:to="loc_cdxs_PfizerMember_ea7255d8-3e9f-44ce-8f03-11cb20890746" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_215a8d60-a755-4aec-a3a2-40e9547c2cc9" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_1d598e71-37ab-4a56-8dfc-f70fd01e9e72" xlink:to="loc_srt_ProductOrServiceAxis_215a8d60-a755-4aec-a3a2-40e9547c2cc9" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_215a8d60-a755-4aec-a3a2-40e9547c2cc9_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_215a8d60-a755-4aec-a3a2-40e9547c2cc9" xlink:to="loc_srt_ProductsAndServicesDomain_215a8d60-a755-4aec-a3a2-40e9547c2cc9_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_5494558a-085e-4d1d-9400-751502cae487" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_215a8d60-a755-4aec-a3a2-40e9547c2cc9" xlink:to="loc_srt_ProductsAndServicesDomain_5494558a-085e-4d1d-9400-751502cae487" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_EnzymeProductMember_06faaf28-9458-404e-9375-11064457fe22" xlink:href="cdxs-20231231.xsd#cdxs_EnzymeProductMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_5494558a-085e-4d1d-9400-751502cae487" xlink:to="loc_cdxs_EnzymeProductMember_06faaf28-9458-404e-9375-11064457fe22" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_e4668ffd-e985-4579-a7f0-a1868c2d5484" xlink:href="cdxs-20231231.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_5494558a-085e-4d1d-9400-751502cae487" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_e4668ffd-e985-4579-a7f0-a1868c2d5484" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_cf4f64f5-3ce2-4b16-b81a-b14d1a8081b8" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_1d598e71-37ab-4a56-8dfc-f70fd01e9e72" xlink:to="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_cf4f64f5-3ce2-4b16-b81a-b14d1a8081b8" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_cf4f64f5-3ce2-4b16-b81a-b14d1a8081b8_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_cf4f64f5-3ce2-4b16-b81a-b14d1a8081b8" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_cf4f64f5-3ce2-4b16-b81a-b14d1a8081b8_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_73a1232a-1bee-437e-a861-fba3b7ad9fc6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_cf4f64f5-3ce2-4b16-b81a-b14d1a8081b8" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_73a1232a-1bee-437e-a861-fba3b7ad9fc6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerMember_b9b22189-7a86-4e04-a9b2-de364cab496f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_73a1232a-1bee-437e-a861-fba3b7ad9fc6" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerMember_b9b22189-7a86-4e04-a9b2-de364cab496f" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByTypeAxis_0e1a7113-e953-4753-8a72-3c6a1bf7cbbf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable_1d598e71-37ab-4a56-8dfc-f70fd01e9e72" xlink:to="loc_us-gaap_ConcentrationRiskByTypeAxis_0e1a7113-e953-4753-8a72-3c6a1bf7cbbf" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_0e1a7113-e953-4753-8a72-3c6a1bf7cbbf_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_0e1a7113-e953-4753-8a72-3c6a1bf7cbbf" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_0e1a7113-e953-4753-8a72-3c6a1bf7cbbf_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_0263596f-af7f-4164-98c6-7bfc49acabb7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_0e1a7113-e953-4753-8a72-3c6a1bf7cbbf" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_0263596f-af7f-4164-98c6-7bfc49acabb7" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CustomerConcentrationRiskMember_d1ec18b4-d4c3-41ef-96d2-014baf34c22e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CustomerConcentrationRiskMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskTypeDomain_0263596f-af7f-4164-98c6-7bfc49acabb7" xlink:to="loc_us-gaap_CustomerConcentrationRiskMember_d1ec18b4-d4c3-41ef-96d2-014baf34c22e" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ContractWithCustomerLiabilityRetainerFee_f6ba99da-7d08-4ef9-a8e8-70dc9520ad11" xlink:href="cdxs-20231231.xsd#cdxs_ContractWithCustomerLiabilityRetainerFee"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_cdxs_ContractWithCustomerLiabilityRetainerFee_f6ba99da-7d08-4ef9-a8e8-70dc9520ad11" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ContractWithCustomerLiabilityRetainerFeeCreditablePercentage_96795690-b2cf-4c43-853f-17e0afb100bf" xlink:href="cdxs-20231231.xsd#cdxs_ContractWithCustomerLiabilityRetainerFeeCreditablePercentage"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_cdxs_ContractWithCustomerLiabilityRetainerFeeCreditablePercentage_96795690-b2cf-4c43-853f-17e0afb100bf" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ContractWithCustomerLiabilityPortionOfRetainerFee_8dbde8f6-5496-4263-afb0-5fcebe0e07de" xlink:href="cdxs-20231231.xsd#cdxs_ContractWithCustomerLiabilityPortionOfRetainerFee"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_cdxs_ContractWithCustomerLiabilityPortionOfRetainerFee_8dbde8f6-5496-4263-afb0-5fcebe0e07de" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_39bde970-54bd-49cd-83c2-2e2b34cda876" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_39bde970-54bd-49cd-83c2-2e2b34cda876" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ContractWithCustomerLiabilityRetainerFeeNonCreditablePercentage_2d21d297-cfb6-40c3-a67b-dd0aeda7cc6b" xlink:href="cdxs-20231231.xsd#cdxs_ContractWithCustomerLiabilityRetainerFeeNonCreditablePercentage"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_cdxs_ContractWithCustomerLiabilityRetainerFeeNonCreditablePercentage_2d21d297-cfb6-40c3-a67b-dd0aeda7cc6b" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_6097e290-4a94-480a-800d-6e90d6cd11ea" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_us-gaap_ContractWithCustomerLiabilityRevenueRecognized_6097e290-4a94-480a-800d-6e90d6cd11ea" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskPercentage1_8f3c6b05-93c7-4ed1-a3d1-9b31e223620b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskPercentage1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_us-gaap_ConcentrationRiskPercentage1_8f3c6b05-93c7-4ed1-a3d1-9b31e223620b" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerLiability_aff4d0f9-bd92-4f72-9282-f660f3b21eed" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ContractWithCustomerLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems_3ac772be-ab53-4ea0-90f0-f2f3be0de868" xlink:to="loc_us-gaap_ContractWithCustomerLiability_aff4d0f9-bd92-4f72-9282-f660f3b21eed" xlink:type="arc" order="7"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/InvestmentsinNonMarketableSecuritiesNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#InvestmentsinNonMarketableSecuritiesNarrativeDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/InvestmentsinNonMarketableSecuritiesNarrativeDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementClassOfStockAxis_36686493-2eed-453c-85f7-a61d0aabc42a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementClassOfStockAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_us-gaap_StatementClassOfStockAxis_36686493-2eed-453c-85f7-a61d0aabc42a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_36686493-2eed-453c-85f7-a61d0aabc42a_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementClassOfStockAxis_36686493-2eed-453c-85f7-a61d0aabc42a" xlink:to="loc_us-gaap_ClassOfStockDomain_36686493-2eed-453c-85f7-a61d0aabc42a_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementClassOfStockAxis_36686493-2eed-453c-85f7-a61d0aabc42a" xlink:to="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeriesB2PreferredStockMember_b2202615-a2d3-4241-a22d-65df8bdf2367" xlink:href="cdxs-20231231.xsd#cdxs_SeriesB2PreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:to="loc_cdxs_SeriesB2PreferredStockMember_b2202615-a2d3-4241-a22d-65df8bdf2367" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SeriesBPreferredStockMember_9a5db662-e7b8-4f97-8ddc-f9b0519ef495" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SeriesBPreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:to="loc_us-gaap_SeriesBPreferredStockMember_9a5db662-e7b8-4f97-8ddc-f9b0519ef495" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockMember_30b2e2d0-4f08-4bc6-b013-3923ea1c45fe" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:to="loc_us-gaap_CommonStockMember_30b2e2d0-4f08-4bc6-b013-3923ea1c45fe" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeriesAAndBPreferredStockMember_d0de0814-bdda-4673-a0d5-e5060ec055e7" xlink:href="cdxs-20231231.xsd#cdxs_SeriesAAndBPreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:to="loc_cdxs_SeriesAAndBPreferredStockMember_d0de0814-bdda-4673-a0d5-e5060ec055e7" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeriesC1PreferredStockMember_843225fa-fe7f-42fd-ae9f-365e60a092a6" xlink:href="cdxs-20231231.xsd#cdxs_SeriesC1PreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:to="loc_cdxs_SeriesC1PreferredStockMember_843225fa-fe7f-42fd-ae9f-365e60a092a6" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CommonStockWarrantsMember_86bbf459-f7bd-46c7-b268-2f8dd139c261" xlink:href="cdxs-20231231.xsd#cdxs_CommonStockWarrantsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:to="loc_cdxs_CommonStockWarrantsMember_86bbf459-f7bd-46c7-b268-2f8dd139c261" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeriesCAndC1PreferredStockMember_d8533abb-b521-42b0-af8d-557909caef2a" xlink:href="cdxs-20231231.xsd#cdxs_SeriesCAndC1PreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_20b6cb59-5a39-450a-b2f8-00bdb3f86010" xlink:to="loc_cdxs_SeriesCAndC1PreferredStockMember_d8533abb-b521-42b0-af8d-557909caef2a" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_494ad604-de9c-4d23-92ff-e4fd272b83ca" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_494ad604-de9c-4d23-92ff-e4fd272b83ca" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_EquityMethodInvesteeNameDomain_494ad604-de9c-4d23-92ff-e4fd272b83ca_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_EquityMethodInvesteeNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_494ad604-de9c-4d23-92ff-e4fd272b83ca" xlink:to="loc_srt_EquityMethodInvesteeNameDomain_494ad604-de9c-4d23-92ff-e4fd272b83ca_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_EquityMethodInvesteeNameDomain_97450cdf-2746-4f47-a244-763365450590" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_EquityMethodInvesteeNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_494ad604-de9c-4d23-92ff-e4fd272b83ca" xlink:to="loc_srt_EquityMethodInvesteeNameDomain_97450cdf-2746-4f47-a244-763365450590" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ArzedaMember_0ee74604-e518-4443-ac89-331bb5cc3254" xlink:href="cdxs-20231231.xsd#cdxs_ArzedaMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_EquityMethodInvesteeNameDomain_97450cdf-2746-4f47-a244-763365450590" xlink:to="loc_cdxs_ArzedaMember_0ee74604-e518-4443-ac89-331bb5cc3254" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MolecularAssembliesIncMember_13feaabe-7f4c-4f11-9bf3-3fcd162df5b1" xlink:href="cdxs-20231231.xsd#cdxs_MolecularAssembliesIncMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_EquityMethodInvesteeNameDomain_97450cdf-2746-4f47-a244-763365450590" xlink:to="loc_cdxs_MolecularAssembliesIncMember_13feaabe-7f4c-4f11-9bf3-3fcd162df5b1" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_5f5d1e84-274c-463e-a9fa-f9b1ade38dc1" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_srt_CounterpartyNameAxis_5f5d1e84-274c-463e-a9fa-f9b1ade38dc1" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_5f5d1e84-274c-463e-a9fa-f9b1ade38dc1_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_5f5d1e84-274c-463e-a9fa-f9b1ade38dc1" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_5f5d1e84-274c-463e-a9fa-f9b1ade38dc1_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_693dd61d-91d2-4708-8ae8-579b1407e71f" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_5f5d1e84-274c-463e-a9fa-f9b1ade38dc1" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_693dd61d-91d2-4708-8ae8-579b1407e71f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MolecularAssembliesIncMember_3f25a298-2a2d-4393-a081-b996ab8a629d" xlink:href="cdxs-20231231.xsd#cdxs_MolecularAssembliesIncMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_693dd61d-91d2-4708-8ae8-579b1407e71f" xlink:to="loc_cdxs_MolecularAssembliesIncMember_3f25a298-2a2d-4393-a081-b996ab8a629d" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_90e0169f-5b92-427b-a3c6-1e07a3046b46" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_90e0169f-5b92-427b-a3c6-1e07a3046b46" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_90e0169f-5b92-427b-a3c6-1e07a3046b46_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_90e0169f-5b92-427b-a3c6-1e07a3046b46" xlink:to="loc_us-gaap_RelatedPartyDomain_90e0169f-5b92-427b-a3c6-1e07a3046b46_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyDomain_b6703308-0df7-458d-9a44-8752b6f50ec0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RelatedPartyTransactionsByRelatedPartyAxis_90e0169f-5b92-427b-a3c6-1e07a3046b46" xlink:to="loc_us-gaap_RelatedPartyDomain_b6703308-0df7-458d-9a44-8752b6f50ec0" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyMember_cde03df9-0afb-4cd6-9c23-33b88fbbb3a6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyDomain_b6703308-0df7-458d-9a44-8752b6f50ec0" xlink:to="loc_us-gaap_RelatedPartyMember_cde03df9-0afb-4cd6-9c23-33b88fbbb3a6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_7862adc3-a265-4ec2-b064-af5d01477bd2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_7862adc3-a265-4ec2-b064-af5d01477bd2" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_7862adc3-a265-4ec2-b064-af5d01477bd2_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_7862adc3-a265-4ec2-b064-af5d01477bd2" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_7862adc3-a265-4ec2-b064-af5d01477bd2_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_6c7fea91-6b81-4a56-b601-6dcb4bff4cf0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_7862adc3-a265-4ec2-b064-af5d01477bd2" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_6c7fea91-6b81-4a56-b601-6dcb4bff4cf0" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeqWellMember_016d670b-788f-4a2a-855f-7d8240f7a32c" xlink:href="cdxs-20231231.xsd#cdxs_SeqWellMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_6c7fea91-6b81-4a56-b601-6dcb4bff4cf0" xlink:to="loc_cdxs_SeqWellMember_016d670b-788f-4a2a-855f-7d8240f7a32c" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ArzedaMember_f34ced99-340e-44d3-bab8-5cbf7cfa821e" xlink:href="cdxs-20231231.xsd#cdxs_ArzedaMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_6c7fea91-6b81-4a56-b601-6dcb4bff4cf0" xlink:to="loc_cdxs_ArzedaMember_f34ced99-340e-44d3-bab8-5cbf7cfa821e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementEquityComponentsAxis_370ef2ef-b5ba-49f1-8e0b-7c2522cd6db9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementEquityComponentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_us-gaap_StatementEquityComponentsAxis_370ef2ef-b5ba-49f1-8e0b-7c2522cd6db9" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquityComponentDomain_370ef2ef-b5ba-49f1-8e0b-7c2522cd6db9_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquityComponentDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementEquityComponentsAxis_370ef2ef-b5ba-49f1-8e0b-7c2522cd6db9" xlink:to="loc_us-gaap_EquityComponentDomain_370ef2ef-b5ba-49f1-8e0b-7c2522cd6db9_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquityComponentDomain_2e910919-56fc-4543-813d-789fcd1ad1bb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquityComponentDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementEquityComponentsAxis_370ef2ef-b5ba-49f1-8e0b-7c2522cd6db9" xlink:to="loc_us-gaap_EquityComponentDomain_2e910919-56fc-4543-813d-789fcd1ad1bb" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockMember_4991ce87-67b5-43ac-8b2b-31a2d9f694a7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_2e910919-56fc-4543-813d-789fcd1ad1bb" xlink:to="loc_us-gaap_CommonStockMember_4991ce87-67b5-43ac-8b2b-31a2d9f694a7" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_dei_LegalEntityAxis_c6710fe3-4270-4175-b660-828c6dc88114" xlink:href="https://xbrl.sec.gov/dei/2023/dei-2023.xsd#dei_LegalEntityAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_dei_LegalEntityAxis_c6710fe3-4270-4175-b660-828c6dc88114" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_dei_EntityDomain_c6710fe3-4270-4175-b660-828c6dc88114_default" xlink:href="https://xbrl.sec.gov/dei/2023/dei-2023.xsd#dei_EntityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_dei_LegalEntityAxis_c6710fe3-4270-4175-b660-828c6dc88114" xlink:to="loc_dei_EntityDomain_c6710fe3-4270-4175-b660-828c6dc88114_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_dei_EntityDomain_f94f7fc7-2b00-442e-87f6-8811ea11b3f2" xlink:href="https://xbrl.sec.gov/dei/2023/dei-2023.xsd#dei_EntityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_dei_LegalEntityAxis_c6710fe3-4270-4175-b660-828c6dc88114" xlink:to="loc_dei_EntityDomain_f94f7fc7-2b00-442e-87f6-8811ea11b3f2" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeqWellMember_26570776-1c69-4066-a1c6-281a4e32c9a8" xlink:href="cdxs-20231231.xsd#cdxs_SeqWellMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_dei_EntityDomain_f94f7fc7-2b00-442e-87f6-8811ea11b3f2" xlink:to="loc_cdxs_SeqWellMember_26570776-1c69-4066-a1c6-281a4e32c9a8" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_595b3a3c-b69d-41b7-a7f2-7c0ba459c500" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductOrServiceAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_17a5c6cc-8180-4cdc-816d-38698f8d3485" xlink:to="loc_srt_ProductOrServiceAxis_595b3a3c-b69d-41b7-a7f2-7c0ba459c500" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_595b3a3c-b69d-41b7-a7f2-7c0ba459c500_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_595b3a3c-b69d-41b7-a7f2-7c0ba459c500" xlink:to="loc_srt_ProductsAndServicesDomain_595b3a3c-b69d-41b7-a7f2-7c0ba459c500_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_7dd68637-b09b-48fc-a83e-f639fa53a0c0" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ProductsAndServicesDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_595b3a3c-b69d-41b7-a7f2-7c0ba459c500" xlink:to="loc_srt_ProductsAndServicesDomain_7dd68637-b09b-48fc-a83e-f639fa53a0c0" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_145a00e4-21b1-4cf1-b987-ac783526065c" xlink:href="cdxs-20231231.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_7dd68637-b09b-48fc-a83e-f639fa53a0c0" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_145a00e4-21b1-4cf1-b987-ac783526065c" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_b3d0aa91-ea72-4fc2-9475-ba807b9ec100" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_b3d0aa91-ea72-4fc2-9475-ba807b9ec100" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConvertibleDebt_ed0ab986-f3c8-40dc-b2f4-19192558c4e9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConvertibleDebt"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_ConvertibleDebt_ed0ab986-f3c8-40dc-b2f4-19192558c4e9" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtConversionConvertedInstrumentSharesIssued1_436a4b8c-7656-407d-9a52-730fc145b5e7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtConversionConvertedInstrumentSharesIssued1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_DebtConversionConvertedInstrumentSharesIssued1_436a4b8c-7656-407d-9a52-730fc145b5e7" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentIncomeAmortizationOfDiscount_2f515481-e6c9-4992-b4ab-267d825376bd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_InvestmentIncomeAmortizationOfDiscount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_InvestmentIncomeAmortizationOfDiscount_2f515481-e6c9-4992-b4ab-267d825376bd" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueShares_658c9409-58d3-44fb-b270-aa14f8d7e214" xlink:href="cdxs-20231231.xsd#cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueShares"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueShares_658c9409-58d3-44fb-b270-aa14f8d7e214" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConvertiblePreferredStockSharesIssuedUponConversion_c05bebe9-146d-44e5-a5df-303983600b44" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConvertiblePreferredStockSharesIssuedUponConversion"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_ConvertiblePreferredStockSharesIssuedUponConversion_c05bebe9-146d-44e5-a5df-303983600b44" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentOwnedBalanceShares_1639ee25-9382-4c24-8003-744de6cf0ea6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_InvestmentOwnedBalanceShares"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_InvestmentOwnedBalanceShares_1639ee25-9382-4c24-8003-744de6cf0ea6" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsToAcquireOtherInvestments_4d589785-d11a-4479-b2bc-1de3b353d2b5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PaymentsToAcquireOtherInvestments"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_PaymentsToAcquireOtherInvestments_4d589785-d11a-4479-b2bc-1de3b353d2b5" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_NoncashOrPartNoncashAcquisitionNoncashFinancialOrEquityInstrumentConsiderationSharesIssued1_bb69a86c-7687-4fb4-a973-0d7b8f5eaa0c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_NoncashOrPartNoncashAcquisitionNoncashFinancialOrEquityInstrumentConsiderationSharesIssued1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_NoncashOrPartNoncashAcquisitionNoncashFinancialOrEquityInstrumentConsiderationSharesIssued1_bb69a86c-7687-4fb4-a973-0d7b8f5eaa0c" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueShares_66a90bc4-1f7d-4357-90cb-5e118b0e7912" xlink:href="cdxs-20231231.xsd#cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueShares"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_565237b3-5dd0-4f6e-9fe8-515b3f6c4d5c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_565237b3-5dd0-4f6e-9fe8-515b3f6c4d5c" xlink:type="arc" order="10"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesIssuedForServices_65144274-7be6-46bd-b9c8-1d04586a2bbf" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockIssuedDuringPeriodSharesIssuedForServices"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesIssuedForServices_65144274-7be6-46bd-b9c8-1d04586a2bbf" xlink:type="arc" order="11"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_177e2ed2-1bda-421b-96ad-2d615954c939" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_177e2ed2-1bda-421b-96ad-2d615954c939" xlink:type="arc" order="12"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueImpairmentLossAnnualAmount_2878ac17-f4c4-4262-9d44-d7299c86b036" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueImpairmentLossAnnualAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueImpairmentLossAnnualAmount_2878ac17-f4c4-4262-9d44-d7299c86b036" xlink:type="arc" order="13"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueUpwardPriceAdjustmentAnnualAmount_603498ef-990f-4306-aebc-fa8e87ee38eb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueUpwardPriceAdjustmentAnnualAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueUpwardPriceAdjustmentAnnualAmount_603498ef-990f-4306-aebc-fa8e87ee38eb" xlink:type="arc" order="14"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueSharesMilestonePaymentsReceived_2d635ab1-a910-4829-8107-c8d1ddb622f6" xlink:href="cdxs-20231231.xsd#cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueSharesMilestonePaymentsReceived"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueSharesMilestonePaymentsReceived_2d635ab1-a910-4829-8107-c8d1ddb622f6" xlink:type="arc" order="15"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueRealizedUpwardDownwardPriceAdjustmentAnnualAmount_3ff8712b-d721-4ef4-91e7-43fb156911e5" xlink:href="cdxs-20231231.xsd#cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueRealizedUpwardDownwardPriceAdjustmentAnnualAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_8815a997-53e3-48e1-961c-0cfe08de8c1e" xlink:to="loc_cdxs_EquitySecuritiesWithoutReadilyDeterminableFairValueRealizedUpwardDownwardPriceAdjustmentAnnualAmount_3ff8712b-d721-4ef4-91e7-43fb156911e5" xlink:type="arc" order="16"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/InvestmentsinNonMarketableSecuritiesCarryingValueandFairValueofSecuritiesDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#InvestmentsinNonMarketableSecuritiesCarryingValueandFairValueofSecuritiesDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/InvestmentsinNonMarketableSecuritiesCarryingValueandFairValueofSecuritiesDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_432d4a23-6543-4489-a647-49fa87577bb8" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_02ab3e37-4502-4d02-9e66-20c17b52b347" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_432d4a23-6543-4489-a647-49fa87577bb8" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_02ab3e37-4502-4d02-9e66-20c17b52b347" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_b25c76a6-a037-42a3-8f18-8a28a6726ae3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueTable_02ab3e37-4502-4d02-9e66-20c17b52b347" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_b25c76a6-a037-42a3-8f18-8a28a6726ae3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_b25c76a6-a037-42a3-8f18-8a28a6726ae3_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_b25c76a6-a037-42a3-8f18-8a28a6726ae3" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_b25c76a6-a037-42a3-8f18-8a28a6726ae3_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_cfaf1f3e-1cc9-4e1c-a708-9ebb5194a144" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_b25c76a6-a037-42a3-8f18-8a28a6726ae3" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_cfaf1f3e-1cc9-4e1c-a708-9ebb5194a144" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MolecularAssembliesIncMember_164ba327-86a0-4882-a15e-267ccc873ac9" xlink:href="cdxs-20231231.xsd#cdxs_MolecularAssembliesIncMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_cfaf1f3e-1cc9-4e1c-a708-9ebb5194a144" xlink:to="loc_cdxs_MolecularAssembliesIncMember_164ba327-86a0-4882-a15e-267ccc873ac9" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SeqWellMember_f6456dc5-263e-422d-b7a2-89fefadb1f8e" xlink:href="cdxs-20231231.xsd#cdxs_SeqWellMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_cfaf1f3e-1cc9-4e1c-a708-9ebb5194a144" xlink:to="loc_cdxs_SeqWellMember_f6456dc5-263e-422d-b7a2-89fefadb1f8e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ArzedaMember_98ace94b-0e71-4b76-b631-eb51917fbad9" xlink:href="cdxs-20231231.xsd#cdxs_ArzedaMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_cfaf1f3e-1cc9-4e1c-a708-9ebb5194a144" xlink:to="loc_cdxs_ArzedaMember_98ace94b-0e71-4b76-b631-eb51917fbad9" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherAggregatedInvestmentsMember_63e97f4b-cb4e-4af7-87e0-e2edf874f11c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherAggregatedInvestmentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_cfaf1f3e-1cc9-4e1c-a708-9ebb5194a144" xlink:to="loc_us-gaap_OtherAggregatedInvestmentsMember_63e97f4b-cb4e-4af7-87e0-e2edf874f11c" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_dc9bf004-97c7-4d14-84bd-d2e8a6699a53" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueLineItems_432d4a23-6543-4489-a647-49fa87577bb8" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_dc9bf004-97c7-4d14-84bd-d2e8a6699a53" xlink:type="arc" order="0"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/FairValueMeasurementsDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#FairValueMeasurementsDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/FairValueMeasurementsDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_7aaef614-fa3d-4490-b9d0-233088489338" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_8c0e2c29-f04b-4f3a-9806-14ffde844738" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_7aaef614-fa3d-4490-b9d0-233088489338" xlink:to="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_8c0e2c29-f04b-4f3a-9806-14ffde844738" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_cb82415d-b640-4e2c-97f3-57d5c031be29" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_8c0e2c29-f04b-4f3a-9806-14ffde844738" xlink:to="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_cb82415d-b640-4e2c-97f3-57d5c031be29" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_cb82415d-b640-4e2c-97f3-57d5c031be29_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_cb82415d-b640-4e2c-97f3-57d5c031be29" xlink:to="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_cb82415d-b640-4e2c-97f3-57d5c031be29_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_467fcc42-e806-4fea-9ee2-92b528d8ac6b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_cb82415d-b640-4e2c-97f3-57d5c031be29" xlink:to="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_467fcc42-e806-4fea-9ee2-92b528d8ac6b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueInputsLevel1Member_b7e79572-5b57-4629-8c37-3e098734db19" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueInputsLevel1Member"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_467fcc42-e806-4fea-9ee2-92b528d8ac6b" xlink:to="loc_us-gaap_FairValueInputsLevel1Member_b7e79572-5b57-4629-8c37-3e098734db19" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueInputsLevel2Member_2c35eaa2-4187-4620-bdfb-4fbe16086fe0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueInputsLevel2Member"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_467fcc42-e806-4fea-9ee2-92b528d8ac6b" xlink:to="loc_us-gaap_FairValueInputsLevel2Member_2c35eaa2-4187-4620-bdfb-4fbe16086fe0" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueInputsLevel3Member_1e192f7d-fd49-4f7c-beae-79d7826f8b80" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FairValueInputsLevel3Member"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_467fcc42-e806-4fea-9ee2-92b528d8ac6b" xlink:to="loc_us-gaap_FairValueInputsLevel3Member_1e192f7d-fd49-4f7c-beae-79d7826f8b80" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsAxis_4348730d-2672-4525-8901-f86bf679ca93" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_8c0e2c29-f04b-4f3a-9806-14ffde844738" xlink:to="loc_us-gaap_CashAndCashEquivalentsAxis_4348730d-2672-4525-8901-f86bf679ca93" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_4348730d-2672-4525-8901-f86bf679ca93_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_CashAndCashEquivalentsAxis_4348730d-2672-4525-8901-f86bf679ca93" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_4348730d-2672-4525-8901-f86bf679ca93_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_e410c25c-5792-485b-9cba-823d2af55f0a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_CashAndCashEquivalentsAxis_4348730d-2672-4525-8901-f86bf679ca93" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_e410c25c-5792-485b-9cba-823d2af55f0a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_MoneyMarketFundsMember_822bd530-0435-4767-a5d5-eb836c2d9b10" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_MoneyMarketFundsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_e410c25c-5792-485b-9cba-823d2af55f0a" xlink:to="loc_us-gaap_MoneyMarketFundsMember_822bd530-0435-4767-a5d5-eb836c2d9b10" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_3706454a-3b8c-4332-b04b-6e5be1d4a512" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_8c0e2c29-f04b-4f3a-9806-14ffde844738" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_3706454a-3b8c-4332-b04b-6e5be1d4a512" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_3706454a-3b8c-4332-b04b-6e5be1d4a512_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_3706454a-3b8c-4332-b04b-6e5be1d4a512" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_3706454a-3b8c-4332-b04b-6e5be1d4a512_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_192452cc-0fee-42ae-bbc6-f45a60011265" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_3706454a-3b8c-4332-b04b-6e5be1d4a512" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_192452cc-0fee-42ae-bbc6-f45a60011265" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConvertibleDebtMember_75e82abb-6b95-4d28-b2b0-b7d326c79aff" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConvertibleDebtMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_192452cc-0fee-42ae-bbc6-f45a60011265" xlink:to="loc_us-gaap_ConvertibleDebtMember_75e82abb-6b95-4d28-b2b0-b7d326c79aff" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancialInstrumentsFinancialAssetsBalanceSheetGroupingsAbstract_bc6583c0-01c6-483e-ace2-14172ec5787f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancialInstrumentsFinancialAssetsBalanceSheetGroupingsAbstract"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_7aaef614-fa3d-4490-b9d0-233088489338" xlink:to="loc_us-gaap_FinancialInstrumentsFinancialAssetsBalanceSheetGroupingsAbstract_bc6583c0-01c6-483e-ace2-14172ec5787f" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_55276d3f-2e7d-4656-aec3-853c2415b94d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FinancialInstrumentsFinancialAssetsBalanceSheetGroupingsAbstract_bc6583c0-01c6-483e-ace2-14172ec5787f" xlink:to="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_55276d3f-2e7d-4656-aec3-853c2415b94d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtSecuritiesAvailableForSaleAllowanceForCreditLossWriteoff_cd17149d-ed10-490d-99f6-158f0405b39a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtSecuritiesAvailableForSaleAllowanceForCreditLossWriteoff"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_7aaef614-fa3d-4490-b9d0-233088489338" xlink:to="loc_us-gaap_DebtSecuritiesAvailableForSaleAllowanceForCreditLossWriteoff_cd17149d-ed10-490d-99f6-158f0405b39a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesGrossUnrealizedLoss_39dd0ce6-0da6-4e65-bf53-38fe287e97d4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AvailableForSaleDebtSecuritiesGrossUnrealizedLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_7aaef614-fa3d-4490-b9d0-233088489338" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesGrossUnrealizedLoss_39dd0ce6-0da6-4e65-bf53-38fe287e97d4" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/BalanceSheetDetailsCashandCashEquivalentsDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#BalanceSheetDetailsCashandCashEquivalentsDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/BalanceSheetDetailsCashandCashEquivalentsDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsLineItems_83816f8d-be19-43d6-9529-386632f32ca4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCashAndCashEquivalentsTable_13c59fb3-38e9-4d59-985c-0d3e1d83bea7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCashAndCashEquivalentsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_83816f8d-be19-43d6-9529-386632f32ca4" xlink:to="loc_us-gaap_ScheduleOfCashAndCashEquivalentsTable_13c59fb3-38e9-4d59-985c-0d3e1d83bea7" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsAxis_524ffd2b-0fbb-401d-aaff-d178c102a6ff" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCashAndCashEquivalentsTable_13c59fb3-38e9-4d59-985c-0d3e1d83bea7" xlink:to="loc_us-gaap_CashAndCashEquivalentsAxis_524ffd2b-0fbb-401d-aaff-d178c102a6ff" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_524ffd2b-0fbb-401d-aaff-d178c102a6ff_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_CashAndCashEquivalentsAxis_524ffd2b-0fbb-401d-aaff-d178c102a6ff" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_524ffd2b-0fbb-401d-aaff-d178c102a6ff_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_1ed290dd-3e35-48d1-9dbe-c53c35e71ec1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_CashAndCashEquivalentsAxis_524ffd2b-0fbb-401d-aaff-d178c102a6ff" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_1ed290dd-3e35-48d1-9dbe-c53c35e71ec1" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_MoneyMarketFundsMember_d210518f-4b5c-4dfe-b88d-e929d9166a9f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_MoneyMarketFundsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_1ed290dd-3e35-48d1-9dbe-c53c35e71ec1" xlink:to="loc_us-gaap_MoneyMarketFundsMember_d210518f-4b5c-4dfe-b88d-e929d9166a9f" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_a4215b26-1689-4aa9-8915-f6b8b4776e59" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_83816f8d-be19-43d6-9529-386632f32ca4" xlink:to="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_a4215b26-1689-4aa9-8915-f6b8b4776e59" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_f676cc92-f76e-4268-9f6e-a19adaf371c2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_83816f8d-be19-43d6-9529-386632f32ca4" xlink:to="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_f676cc92-f76e-4268-9f6e-a19adaf371c2" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/BalanceSheetDetailsNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#BalanceSheetDetailsNarrativeDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/BalanceSheetDetailsNarrativeDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfCashAndCashEquivalentsTable_e3ceb4e1-9c8a-480f-91ca-7330c155ec39" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfCashAndCashEquivalentsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_ScheduleOfCashAndCashEquivalentsTable_e3ceb4e1-9c8a-480f-91ca-7330c155ec39" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsAxis_c19e2669-0439-4984-adcc-1908aceda008" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCashAndCashEquivalentsTable_e3ceb4e1-9c8a-480f-91ca-7330c155ec39" xlink:to="loc_us-gaap_CashAndCashEquivalentsAxis_c19e2669-0439-4984-adcc-1908aceda008" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_c19e2669-0439-4984-adcc-1908aceda008_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_CashAndCashEquivalentsAxis_c19e2669-0439-4984-adcc-1908aceda008" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_c19e2669-0439-4984-adcc-1908aceda008_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_b4ad2a02-02cf-4b8a-8134-f1dfcbd5446b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_CashAndCashEquivalentsAxis_c19e2669-0439-4984-adcc-1908aceda008" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_b4ad2a02-02cf-4b8a-8134-f1dfcbd5446b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_MoneyMarketFundsMember_9fa9f19b-a00d-4b5f-acc2-e05f4e241b3b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_MoneyMarketFundsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_b4ad2a02-02cf-4b8a-8134-f1dfcbd5446b" xlink:to="loc_us-gaap_MoneyMarketFundsMember_9fa9f19b-a00d-4b5f-acc2-e05f4e241b3b" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashMember_3ef07f88-4636-4cc6-8c8f-bcdcf4a73366" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_b4ad2a02-02cf-4b8a-8134-f1dfcbd5446b" xlink:to="loc_us-gaap_CashMember_3ef07f88-4636-4cc6-8c8f-bcdcf4a73366" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_95251e90-0e95-40df-8958-26311d7b96ce" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfCashAndCashEquivalentsTable_e3ceb4e1-9c8a-480f-91ca-7330c155ec39" xlink:to="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_95251e90-0e95-40df-8958-26311d7b96ce" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_95251e90-0e95-40df-8958-26311d7b96ce_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_95251e90-0e95-40df-8958-26311d7b96ce" xlink:to="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_95251e90-0e95-40df-8958-26311d7b96ce_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_72446bf4-4b80-49d0-9251-5ac1f2cbcc86" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_95251e90-0e95-40df-8958-26311d7b96ce" xlink:to="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_72446bf4-4b80-49d0-9251-5ac1f2cbcc86" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SanCarlosMember_7ecbbe20-2e99-4b95-8d26-2e64e1716a38" xlink:href="cdxs-20231231.xsd#cdxs_SanCarlosMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_72446bf4-4b80-49d0-9251-5ac1f2cbcc86" xlink:to="loc_cdxs_SanCarlosMember_7ecbbe20-2e99-4b95-8d26-2e64e1716a38" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_8a095e8c-b7c2-4663-bf62-72366fb989bb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_8a095e8c-b7c2-4663-bf62-72366fb989bb" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_102a4452-ff14-48af-9cc0-3df91644eb56" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_102a4452-ff14-48af-9cc0-3df91644eb56" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PrepaidExpenseCurrent_a8771674-6cc7-4cf9-9d39-58c4831f4235" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PrepaidExpenseCurrent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_PrepaidExpenseCurrent_a8771674-6cc7-4cf9-9d39-58c4831f4235" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherAssetsCurrent_01a1ffa8-dce3-4a77-8a65-f4ab202ead60" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherAssetsCurrent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_OtherAssetsCurrent_01a1ffa8-dce3-4a77-8a65-f4ab202ead60" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AssetImpairmentCharges_803995bd-c5b7-4ba6-860f-ffe83206aa1e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AssetImpairmentCharges"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_AssetImpairmentCharges_803995bd-c5b7-4ba6-860f-ffe83206aa1e" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ImpairmentOfLeasehold_62324801-9343-4cf9-a4c5-f9cbfb6f60a3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ImpairmentOfLeasehold"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_ImpairmentOfLeasehold_62324801-9343-4cf9-a4c5-f9cbfb6f60a3" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GoodwillImpairmentLoss_419d92cd-ba0a-4dca-a75f-3c53b262d00d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GoodwillImpairmentLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_GoodwillImpairmentLoss_419d92cd-ba0a-4dca-a75f-3c53b262d00d" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_Goodwill_eff6b933-81f7-48c2-ae7c-99f715df9227" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_Goodwill"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CashAndCashEquivalentsLineItems_438ac0a2-1552-48af-8eeb-1149b20acf92" xlink:to="loc_us-gaap_Goodwill_eff6b933-81f7-48c2-ae7c-99f715df9227" xlink:type="arc" order="7"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/BalanceSheetDetailsPropertyandEquipmentnetDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#BalanceSheetDetailsPropertyandEquipmentnetDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/BalanceSheetDetailsPropertyandEquipmentnetDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentLineItems_f23dd45f-98c4-430b-a11c-621e4f7ea441" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_9b1ce47c-2afb-4933-936f-160fd67df366" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_f23dd45f-98c4-430b-a11c-621e4f7ea441" xlink:to="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_9b1ce47c-2afb-4933-936f-160fd67df366" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_8ca2710f-96a2-4de0-9594-954cfd6ebed3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_9b1ce47c-2afb-4933-936f-160fd67df366" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_8ca2710f-96a2-4de0-9594-954cfd6ebed3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_8ca2710f-96a2-4de0-9594-954cfd6ebed3_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_8ca2710f-96a2-4de0-9594-954cfd6ebed3" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_8ca2710f-96a2-4de0-9594-954cfd6ebed3_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_ea97149a-5380-495d-8fbd-1e730df5aafb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_8ca2710f-96a2-4de0-9594-954cfd6ebed3" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_ea97149a-5380-495d-8fbd-1e730df5aafb" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_LaboratoryEquipmentMember_72dfd152-b3a5-4b3f-8f17-831ee60ac98e" xlink:href="cdxs-20231231.xsd#cdxs_LaboratoryEquipmentMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_ea97149a-5380-495d-8fbd-1e730df5aafb" xlink:to="loc_cdxs_LaboratoryEquipmentMember_72dfd152-b3a5-4b3f-8f17-831ee60ac98e" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LeaseholdImprovementsMember_6a581825-53d7-4273-90e1-faf473c5857f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LeaseholdImprovementsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_ea97149a-5380-495d-8fbd-1e730df5aafb" xlink:to="loc_us-gaap_LeaseholdImprovementsMember_6a581825-53d7-4273-90e1-faf473c5857f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ComputerEquipmentMember_049482f8-65d3-4596-93ab-5b7372a09121" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ComputerEquipmentMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_ea97149a-5380-495d-8fbd-1e730df5aafb" xlink:to="loc_us-gaap_ComputerEquipmentMember_049482f8-65d3-4596-93ab-5b7372a09121" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_OfficeEquipmentAndFurnitureMember_76aa5262-ea3c-484b-96f5-6e5ad67d733e" xlink:href="cdxs-20231231.xsd#cdxs_OfficeEquipmentAndFurnitureMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_ea97149a-5380-495d-8fbd-1e730df5aafb" xlink:to="loc_cdxs_OfficeEquipmentAndFurnitureMember_76aa5262-ea3c-484b-96f5-6e5ad67d733e" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConstructionInProgressMember_c54481a7-702f-484a-a4db-583fff384b5a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConstructionInProgressMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_ea97149a-5380-495d-8fbd-1e730df5aafb" xlink:to="loc_us-gaap_ConstructionInProgressMember_c54481a7-702f-484a-a4db-583fff384b5a" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentNetByTypeAbstract_3ba352f5-f660-458e-b374-31a090217034" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentNetByTypeAbstract"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_f23dd45f-98c4-430b-a11c-621e4f7ea441" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentNetByTypeAbstract_3ba352f5-f660-458e-b374-31a090217034" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentGross_8dae9d18-da2f-49b5-91e9-18c6ddf69b28" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentGross"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentNetByTypeAbstract_3ba352f5-f660-458e-b374-31a090217034" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentGross_8dae9d18-da2f-49b5-91e9-18c6ddf69b28" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment_92f482b3-f318-450b-bcf0-e10b1338f350" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentNetByTypeAbstract_3ba352f5-f660-458e-b374-31a090217034" xlink:to="loc_us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment_92f482b3-f318-450b-bcf0-e10b1338f350" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentNet_31244f88-9ab9-425c-85cb-0443bd5d81c9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentNet"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentNetByTypeAbstract_3ba352f5-f660-458e-b374-31a090217034" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentNet_31244f88-9ab9-425c-85cb-0443bd5d81c9" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentDisposals_fc80e52e-874f-4298-ae15-b2769a6c403d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PropertyPlantAndEquipmentDisposals"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_f23dd45f-98c4-430b-a11c-621e4f7ea441" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentDisposals_fc80e52e-874f-4298-ae15-b2769a6c403d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_Depreciation_e4990955-44a0-4b5c-82bb-52d6deaad9a9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_Depreciation"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_f23dd45f-98c4-430b-a11c-621e4f7ea441" xlink:to="loc_us-gaap_Depreciation_e4990955-44a0-4b5c-82bb-52d6deaad9a9" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/StockbasedCompensationNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#StockbasedCompensationNarrativeDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/StockbasedCompensationNarrativeDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_1115c0d7-4bd6-4371-87cb-8a8ffb4a1158" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_1115c0d7-4bd6-4371-87cb-8a8ffb4a1158" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PlanNameAxis_2004d631-76bc-4a0a-8ba7-858082749912" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PlanNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_1115c0d7-4bd6-4371-87cb-8a8ffb4a1158" xlink:to="loc_us-gaap_PlanNameAxis_2004d631-76bc-4a0a-8ba7-858082749912" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PlanNameDomain_2004d631-76bc-4a0a-8ba7-858082749912_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_PlanNameAxis_2004d631-76bc-4a0a-8ba7-858082749912" xlink:to="loc_us-gaap_PlanNameDomain_2004d631-76bc-4a0a-8ba7-858082749912_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_PlanNameAxis_2004d631-76bc-4a0a-8ba7-858082749912" xlink:to="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2022InducementPlanMember_acfd7376-14ce-4af9-bf4d-c1e2a0a6cc04" xlink:href="cdxs-20231231.xsd#cdxs_A2022InducementPlanMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2022InducementPlanMember_acfd7376-14ce-4af9-bf4d-c1e2a0a6cc04" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2019PlanMember_9feea540-d3af-44cc-9e11-2b5476944dce" xlink:href="cdxs-20231231.xsd#cdxs_A2019PlanMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2019PlanMember_9feea540-d3af-44cc-9e11-2b5476944dce" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2019AmendedPlanMember_81cde68a-0b69-4b38-a54e-0044ae0207d5" xlink:href="cdxs-20231231.xsd#cdxs_A2019AmendedPlanMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2019AmendedPlanMember_81cde68a-0b69-4b38-a54e-0044ae0207d5" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2022PSUMember_923e732e-6cc5-4348-b0d4-bf992a0d8f74" xlink:href="cdxs-20231231.xsd#cdxs_A2022PSUMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2022PSUMember_923e732e-6cc5-4348-b0d4-bf992a0d8f74" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2022PBOMember_739076e6-44f8-4716-8fc9-f6f5adeebb17" xlink:href="cdxs-20231231.xsd#cdxs_A2022PBOMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2022PBOMember_739076e6-44f8-4716-8fc9-f6f5adeebb17" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2022PSUAnd2022PBOMember_a451d8da-0109-471c-8876-c6333dc33429" xlink:href="cdxs-20231231.xsd#cdxs_A2022PSUAnd2022PBOMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2022PSUAnd2022PBOMember_a451d8da-0109-471c-8876-c6333dc33429" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2021PSUMember_8428fb3b-5760-47b1-bc8b-4d3b02bf1b1e" xlink:href="cdxs-20231231.xsd#cdxs_A2021PSUMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2021PSUMember_8428fb3b-5760-47b1-bc8b-4d3b02bf1b1e" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2021PBOMember_73329b2b-0dec-48b8-9b26-4b9527dcaf3c" xlink:href="cdxs-20231231.xsd#cdxs_A2021PBOMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2021PBOMember_73329b2b-0dec-48b8-9b26-4b9527dcaf3c" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A2021PSUAnd2021PBOMember_3c6c2888-6223-4839-8bc5-110c1c0a6316" xlink:href="cdxs-20231231.xsd#cdxs_A2021PSUAnd2021PBOMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PlanNameDomain_0a4fae5e-7315-45a9-ad40-590e801d3589" xlink:to="loc_cdxs_A2021PSUAnd2021PBOMember_3c6c2888-6223-4839-8bc5-110c1c0a6316" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AwardTypeAxis_492f8627-992d-437f-a518-661539e603d2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AwardTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_1115c0d7-4bd6-4371-87cb-8a8ffb4a1158" xlink:to="loc_us-gaap_AwardTypeAxis_492f8627-992d-437f-a518-661539e603d2" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_492f8627-992d-437f-a518-661539e603d2_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AwardTypeAxis_492f8627-992d-437f-a518-661539e603d2" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_492f8627-992d-437f-a518-661539e603d2_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AwardTypeAxis_492f8627-992d-437f-a518-661539e603d2" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_874a4a45-1120-4ad5-a8be-c03f4a6da9b3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_us-gaap_EmployeeStockMember_874a4a45-1120-4ad5-a8be-c03f4a6da9b3" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_IncentiveStockOptionsMember_65d46299-f2d3-48af-ac16-9e3d552d748f" xlink:href="cdxs-20231231.xsd#cdxs_IncentiveStockOptionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_cdxs_IncentiveStockOptionsMember_65d46299-f2d3-48af-ac16-9e3d552d748f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_NonStatutoryStockOptionsMember_249b2b1a-532d-4233-9ed2-34fabaf0e467" xlink:href="cdxs-20231231.xsd#cdxs_NonStatutoryStockOptionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_cdxs_NonStatutoryStockOptionsMember_249b2b1a-532d-4233-9ed2-34fabaf0e467" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockOptionMember_ae4163d2-3a54-4053-8075-80ff6ec57208" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockOptionMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_us-gaap_EmployeeStockOptionMember_ae4163d2-3a54-4053-8075-80ff6ec57208" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedStockUnitsRSUMember_804d5d46-68c0-42de-81d8-589320be0ecd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedStockUnitsRSUMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_us-gaap_RestrictedStockUnitsRSUMember_804d5d46-68c0-42de-81d8-589320be0ecd" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PerformanceSharesMember_adc1b6a9-1c55-434c-af06-cb24234929c9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PerformanceSharesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_us-gaap_PerformanceSharesMember_adc1b6a9-1c55-434c-af06-cb24234929c9" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceShareUnitsPSUsMember_fb401cd4-365d-45df-8413-992c354367f5" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceShareUnitsPSUsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_cdxs_PerformanceShareUnitsPSUsMember_fb401cd4-365d-45df-8413-992c354367f5" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceBasedOptionsPBOsMember_92592338-43bb-40b3-a05a-d39000f4fcad" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceBasedOptionsPBOsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_cdxs_PerformanceBasedOptionsPBOsMember_92592338-43bb-40b3-a05a-d39000f4fcad" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedStockMember_cb5d82cf-afd0-4f88-a5fd-9b747098774f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_us-gaap_RestrictedStockMember_cb5d82cf-afd0-4f88-a5fd-9b747098774f" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceStockUnitsMember_1b22beb0-8a4d-4c1e-afb5-5d869dcbeff2" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceStockUnitsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_ac854530-dc97-4ca0-bd2c-8fdf3616117d" xlink:to="loc_cdxs_PerformanceStockUnitsMember_1b22beb0-8a4d-4c1e-afb5-5d869dcbeff2" xlink:type="arc" order="9"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_VestingAxis_deb20dc4-724a-42ad-a254-902aa408dcc9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_VestingAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_1115c0d7-4bd6-4371-87cb-8a8ffb4a1158" xlink:to="loc_us-gaap_VestingAxis_deb20dc4-724a-42ad-a254-902aa408dcc9" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_VestingDomain_deb20dc4-724a-42ad-a254-902aa408dcc9_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_VestingDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_VestingAxis_deb20dc4-724a-42ad-a254-902aa408dcc9" xlink:to="loc_us-gaap_VestingDomain_deb20dc4-724a-42ad-a254-902aa408dcc9_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_VestingDomain_06685d79-79dc-4092-b4d2-cf33c6a2188f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_VestingDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_VestingAxis_deb20dc4-724a-42ad-a254-902aa408dcc9" xlink:to="loc_us-gaap_VestingDomain_06685d79-79dc-4092-b4d2-cf33c6a2188f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationAwardTrancheOneMember_d30da94d-2c0d-49c7-bd9d-ed835f856aa5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationAwardTrancheOneMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_VestingDomain_06685d79-79dc-4092-b4d2-cf33c6a2188f" xlink:to="loc_us-gaap_ShareBasedCompensationAwardTrancheOneMember_d30da94d-2c0d-49c7-bd9d-ed835f856aa5" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationAwardTrancheTwoMember_e599e6ae-b88c-4ffa-b59b-3f087ca4508d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationAwardTrancheTwoMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_VestingDomain_06685d79-79dc-4092-b4d2-cf33c6a2188f" xlink:to="loc_us-gaap_ShareBasedCompensationAwardTrancheTwoMember_e599e6ae-b88c-4ffa-b59b-3f087ca4508d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusAxis_9377ef43-d6f6-420e-9c7f-1023f9f84d0c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_1115c0d7-4bd6-4371-87cb-8a8ffb4a1158" xlink:to="loc_us-gaap_GranteeStatusAxis_9377ef43-d6f6-420e-9c7f-1023f9f84d0c" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusDomain_9377ef43-d6f6-420e-9c7f-1023f9f84d0c_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_GranteeStatusAxis_9377ef43-d6f6-420e-9c7f-1023f9f84d0c" xlink:to="loc_us-gaap_GranteeStatusDomain_9377ef43-d6f6-420e-9c7f-1023f9f84d0c_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusDomain_e30fe4b6-38c5-4009-bd0c-26d62d122517" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_GranteeStatusAxis_9377ef43-d6f6-420e-9c7f-1023f9f84d0c" xlink:to="loc_us-gaap_GranteeStatusDomain_e30fe4b6-38c5-4009-bd0c-26d62d122517" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_93ecd198-3b7d-46da-86d5-5ca820617406" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedPaymentArrangementNonemployeeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_GranteeStatusDomain_e30fe4b6-38c5-4009-bd0c-26d62d122517" xlink:to="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_93ecd198-3b7d-46da-86d5-5ca820617406" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAuthorized_fbef52b8-9917-44b1-9cea-b77c8df189ed" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAuthorized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAuthorized_fbef52b8-9917-44b1-9cea-b77c8df189ed" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant_a86a76bf-ba04-448a-b5ea-5303450087fe" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant_a86a76bf-ba04-448a-b5ea-5303450087fe" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized_ab972c9a-d54d-4fe9-9174-c8f7a190ccde" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized_ab972c9a-d54d-4fe9-9174-c8f7a190ccde" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockCapitalSharesReservedForFutureIssuance_f0440a83-7dcc-4a1c-a459-84dac45090fd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockCapitalSharesReservedForFutureIssuance"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_CommonStockCapitalSharesReservedForFutureIssuance_f0440a83-7dcc-4a1c-a459-84dac45090fd" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShareBasedCompensationArrangementBySharebasedPaymentAwardConsecutiveOfferingPeriod_2e16c754-2467-4097-8afa-069a8c3728ac" xlink:href="cdxs-20231231.xsd#cdxs_ShareBasedCompensationArrangementBySharebasedPaymentAwardConsecutiveOfferingPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_ShareBasedCompensationArrangementBySharebasedPaymentAwardConsecutiveOfferingPeriod_2e16c754-2467-4097-8afa-069a8c3728ac" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardPurchasePriceOfCommonStockPercent_862cbd3f-514a-459f-bf15-edff17349156" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardPurchasePriceOfCommonStockPercent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardPurchasePriceOfCommonStockPercent_862cbd3f-514a-459f-bf15-edff17349156" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardMaximumEmployeeSubscriptionAmount_f86c17da-d435-4551-afc6-20210055e2d9" xlink:href="cdxs-20231231.xsd#cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardMaximumEmployeeSubscriptionAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardMaximumEmployeeSubscriptionAmount_f86c17da-d435-4551-afc6-20210055e2d9" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AllocatedShareBasedCompensationExpense_ca85801d-ecdd-406f-b107-85f5ad583eeb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AllocatedShareBasedCompensationExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_AllocatedShareBasedCompensationExpense_ca85801d-ecdd-406f-b107-85f5ad583eeb" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PercentOfVotingInterestsThresholdToTriggerHigherExercisePrice_30141126-4158-4869-a13b-c9747057ad4c" xlink:href="cdxs-20231231.xsd#cdxs_PercentOfVotingInterestsThresholdToTriggerHigherExercisePrice"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_PercentOfVotingInterestsThresholdToTriggerHigherExercisePrice_30141126-4158-4869-a13b-c9747057ad4c" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardPurchasePriceOfCommonStockAboveMinimumThresholdPercent_f80f3117-565a-4e9f-a6d0-b6517f3d2acf" xlink:href="cdxs-20231231.xsd#cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardPurchasePriceOfCommonStockAboveMinimumThresholdPercent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardPurchasePriceOfCommonStockAboveMinimumThresholdPercent_f80f3117-565a-4e9f-a6d0-b6517f3d2acf" xlink:type="arc" order="9"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod_44d8f9fa-bb2a-4436-b5e5-2d51a9eb3489" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod_44d8f9fa-bb2a-4436-b5e5-2d51a9eb3489" xlink:type="arc" order="10"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1_f7d1c43e-8559-4094-8baf-5fc3718bd577" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1_f7d1c43e-8559-4094-8baf-5fc3718bd577" xlink:type="arc" order="11"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage_07af2ccc-9085-4b62-96d6-422389eda30d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage_07af2ccc-9085-4b62-96d6-422389eda30d" xlink:type="arc" order="12"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriodUponTerminationOfService_bc984aa6-b969-4264-892f-6d234f08c8d1" xlink:href="cdxs-20231231.xsd#cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriodUponTerminationOfService"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriodUponTerminationOfService_bc984aa6-b969-4264-892f-6d234f08c8d1" xlink:type="arc" order="13"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardNumberofInstallments_d41860b5-6657-4365-8a3d-7f2b62d7430e" xlink:href="cdxs-20231231.xsd#cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardNumberofInstallments"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardNumberofInstallments_d41860b5-6657-4365-8a3d-7f2b62d7430e" xlink:type="arc" order="14"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardPerformanceGoalsAchievedSuperiorLevelSharesEligibleToVestMultiplier_1084d702-7374-4179-bd85-41e467fa8e12" xlink:href="cdxs-20231231.xsd#cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardPerformanceGoalsAchievedSuperiorLevelSharesEligibleToVestMultiplier"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardPerformanceGoalsAchievedSuperiorLevelSharesEligibleToVestMultiplier_1084d702-7374-4179-bd85-41e467fa8e12" xlink:type="arc" order="15"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardPerformanceAwardsThresholdLevelNumberofSharesMultiplier_309ddf46-4a85-42bc-87da-b120f7487b0f" xlink:href="cdxs-20231231.xsd#cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardPerformanceAwardsThresholdLevelNumberofSharesMultiplier"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardPerformanceAwardsThresholdLevelNumberofSharesMultiplier_309ddf46-4a85-42bc-87da-b120f7487b0f" xlink:type="arc" order="16"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod_b01d98cd-29ba-4684-a6b5-9f845cbdb219" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod_b01d98cd-29ba-4684-a6b5-9f845cbdb219" xlink:type="arc" order="17"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardEstimatedPerformanceGoalAchievementRate_cbb65de5-719c-412d-adc9-67da79808550" xlink:href="cdxs-20231231.xsd#cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardEstimatedPerformanceGoalAchievementRate"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardEstimatedPerformanceGoalAchievementRate_cbb65de5-719c-412d-adc9-67da79808550" xlink:type="arc" order="18"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross_9e4d5d6e-6878-4ff8-9c5b-18b9de5ea6c8" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross_9e4d5d6e-6878-4ff8-9c5b-18b9de5ea6c8" xlink:type="arc" order="19"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisesInPeriodTotalIntrinsicValue_c9a8e623-7eb8-4fef-8a9d-1e799540f0e9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisesInPeriodTotalIntrinsicValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisesInPeriodTotalIntrinsicValue_c9a8e623-7eb8-4fef-8a9d-1e799540f0e9" xlink:type="arc" order="20"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue_0810d602-ab84-4957-89f3-ff1a688374d6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue_0810d602-ab84-4957-89f3-ff1a688374d6" xlink:type="arc" order="21"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions_9a451461-48ae-4d8b-a9f4-abc07381ac2b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions_9a451461-48ae-4d8b-a9f4-abc07381ac2b" xlink:type="arc" order="22"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1_7d95ceff-3976-4020-a997-014f846d7775" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1_7d95ceff-3976-4020-a997-014f846d7775" xlink:type="arc" order="23"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateIntrinsicValueVested_5624c47f-4344-458d-8e88-39b34dda75c9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateIntrinsicValueVested"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateIntrinsicValueVested_5624c47f-4344-458d-8e88-39b34dda75c9" xlink:type="arc" order="24"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions_adc54a07-6d00-4eab-8272-c698ea65d20c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_6c95660f-a26b-45ed-b6ac-10672e226aa5" xlink:to="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions_adc54a07-6d00-4eab-8272-c698ea65d20c" xlink:type="arc" order="25"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/StockbasedCompensationStockBasedCompensationExpenseDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#StockbasedCompensationStockBasedCompensationExpenseDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/StockbasedCompensationStockBasedCompensationExpenseDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_0d64d03d-8711-49a4-8175-254c6cc62fe2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_8781eb19-f8a0-4e5c-9602-30309291e0c3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_0d64d03d-8711-49a4-8175-254c6cc62fe2" xlink:to="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_8781eb19-f8a0-4e5c-9602-30309291e0c3" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeStatementLocationAxis_8e53ec10-16bc-4f34-a5f4-0448ec00f18d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeStatementLocationAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_8781eb19-f8a0-4e5c-9602-30309291e0c3" xlink:to="loc_us-gaap_IncomeStatementLocationAxis_8e53ec10-16bc-4f34-a5f4-0448ec00f18d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeStatementLocationDomain_8e53ec10-16bc-4f34-a5f4-0448ec00f18d_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeStatementLocationDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_IncomeStatementLocationAxis_8e53ec10-16bc-4f34-a5f4-0448ec00f18d" xlink:to="loc_us-gaap_IncomeStatementLocationDomain_8e53ec10-16bc-4f34-a5f4-0448ec00f18d_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeStatementLocationDomain_7685cb1e-8703-4d2a-83f8-e6064e318b78" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeStatementLocationDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_IncomeStatementLocationAxis_8e53ec10-16bc-4f34-a5f4-0448ec00f18d" xlink:to="loc_us-gaap_IncomeStatementLocationDomain_7685cb1e-8703-4d2a-83f8-e6064e318b78" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CostOfSalesMember_9075c334-ad9e-4158-afd1-a45042c03249" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CostOfSalesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncomeStatementLocationDomain_7685cb1e-8703-4d2a-83f8-e6064e318b78" xlink:to="loc_us-gaap_CostOfSalesMember_9075c334-ad9e-4158-afd1-a45042c03249" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentExpenseMember_9ac57c57-0b82-482c-ad35-69e3f08556fb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ResearchAndDevelopmentExpenseMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncomeStatementLocationDomain_7685cb1e-8703-4d2a-83f8-e6064e318b78" xlink:to="loc_us-gaap_ResearchAndDevelopmentExpenseMember_9ac57c57-0b82-482c-ad35-69e3f08556fb" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SellingGeneralAndAdministrativeExpensesMember_af00ebb5-f19e-4ff5-aec2-0030b02a70ba" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SellingGeneralAndAdministrativeExpensesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncomeStatementLocationDomain_7685cb1e-8703-4d2a-83f8-e6064e318b78" xlink:to="loc_us-gaap_SellingGeneralAndAdministrativeExpensesMember_af00ebb5-f19e-4ff5-aec2-0030b02a70ba" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AwardTypeAxis_c8fbe539-f856-44f2-b457-aa0d6549b9eb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AwardTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_8781eb19-f8a0-4e5c-9602-30309291e0c3" xlink:to="loc_us-gaap_AwardTypeAxis_c8fbe539-f856-44f2-b457-aa0d6549b9eb" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_c8fbe539-f856-44f2-b457-aa0d6549b9eb_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AwardTypeAxis_c8fbe539-f856-44f2-b457-aa0d6549b9eb" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_c8fbe539-f856-44f2-b457-aa0d6549b9eb_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd0a3e00-c499-451a-8d6b-53908a83334e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AwardTypeAxis_c8fbe539-f856-44f2-b457-aa0d6549b9eb" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd0a3e00-c499-451a-8d6b-53908a83334e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockOptionMember_33b44fde-3abe-4ca8-93ed-b484ad2ccf1d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockOptionMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd0a3e00-c499-451a-8d6b-53908a83334e" xlink:to="loc_us-gaap_EmployeeStockOptionMember_33b44fde-3abe-4ca8-93ed-b484ad2ccf1d" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RSUsAndRSAsMember_ac4ca763-e3ee-488b-9116-5b71894ce48a" xlink:href="cdxs-20231231.xsd#cdxs_RSUsAndRSAsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd0a3e00-c499-451a-8d6b-53908a83334e" xlink:to="loc_cdxs_RSUsAndRSAsMember_ac4ca763-e3ee-488b-9116-5b71894ce48a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceStockUnitsMember_d22c77d9-5ec9-42ca-8817-d77928f5fad4" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceStockUnitsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd0a3e00-c499-451a-8d6b-53908a83334e" xlink:to="loc_cdxs_PerformanceStockUnitsMember_d22c77d9-5ec9-42ca-8817-d77928f5fad4" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceBasedOptionsPBOsMember_d11baf51-12eb-47f8-8a38-1e6e718a59ec" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceBasedOptionsPBOsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd0a3e00-c499-451a-8d6b-53908a83334e" xlink:to="loc_cdxs_PerformanceBasedOptionsPBOsMember_d11baf51-12eb-47f8-8a38-1e6e718a59ec" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_af3d2cb8-c916-4ce5-bf16-ba885b4bef80" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd0a3e00-c499-451a-8d6b-53908a83334e" xlink:to="loc_us-gaap_EmployeeStockMember_af3d2cb8-c916-4ce5-bf16-ba885b4bef80" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationAggregateDisclosuresAbstract_3a0fea6e-925f-42e2-917a-554d7e10f748" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeServiceShareBasedCompensationAggregateDisclosuresAbstract"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_0d64d03d-8711-49a4-8175-254c6cc62fe2" xlink:to="loc_us-gaap_EmployeeServiceShareBasedCompensationAggregateDisclosuresAbstract_3a0fea6e-925f-42e2-917a-554d7e10f748" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensation_71102dae-dba0-40ef-8938-ce4cf79d5e0d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensation"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EmployeeServiceShareBasedCompensationAggregateDisclosuresAbstract_3a0fea6e-925f-42e2-917a-554d7e10f748" xlink:to="loc_us-gaap_ShareBasedCompensation_71102dae-dba0-40ef-8938-ce4cf79d5e0d" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/StockbasedCompensationAssumptionsUsedDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#StockbasedCompensationAssumptionsUsedDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/StockbasedCompensationAssumptionsUsedDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_28656564-14ec-4b8f-a90b-1643771ab85c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_617ad648-d3bb-462d-91db-b7f2f213e2ce" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_28656564-14ec-4b8f-a90b-1643771ab85c" xlink:to="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_617ad648-d3bb-462d-91db-b7f2f213e2ce" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AwardTypeAxis_a3e14cea-26cd-4a47-92ea-29f3b1db50d5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AwardTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_617ad648-d3bb-462d-91db-b7f2f213e2ce" xlink:to="loc_us-gaap_AwardTypeAxis_a3e14cea-26cd-4a47-92ea-29f3b1db50d5" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_a3e14cea-26cd-4a47-92ea-29f3b1db50d5_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AwardTypeAxis_a3e14cea-26cd-4a47-92ea-29f3b1db50d5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_a3e14cea-26cd-4a47-92ea-29f3b1db50d5_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_362ae6c3-4ce5-49b1-a8bf-c85290a01b53" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AwardTypeAxis_a3e14cea-26cd-4a47-92ea-29f3b1db50d5" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_362ae6c3-4ce5-49b1-a8bf-c85290a01b53" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockOptionMember_fb428f6b-795a-40b7-be51-584229534b70" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockOptionMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_362ae6c3-4ce5-49b1-a8bf-c85290a01b53" xlink:to="loc_us-gaap_EmployeeStockOptionMember_fb428f6b-795a-40b7-be51-584229534b70" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_ab160b72-5db3-45d8-b782-21263eb26df2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedPaymentArrangementNonemployeeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_362ae6c3-4ce5-49b1-a8bf-c85290a01b53" xlink:to="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_ab160b72-5db3-45d8-b782-21263eb26df2" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceBasedOptionsPBOsMember_3b54ab84-7b4c-4c71-a1f1-b7d743de686a" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceBasedOptionsPBOsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_362ae6c3-4ce5-49b1-a8bf-c85290a01b53" xlink:to="loc_cdxs_PerformanceBasedOptionsPBOsMember_3b54ab84-7b4c-4c71-a1f1-b7d743de686a" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_6bb4b825-f6bc-4839-b1a6-5e8f10b6ec87" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_362ae6c3-4ce5-49b1-a8bf-c85290a01b53" xlink:to="loc_us-gaap_EmployeeStockMember_6bb4b825-f6bc-4839-b1a6-5e8f10b6ec87" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusAxis_0a179b97-0749-49e2-adba-4ee3acd21846" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_617ad648-d3bb-462d-91db-b7f2f213e2ce" xlink:to="loc_us-gaap_GranteeStatusAxis_0a179b97-0749-49e2-adba-4ee3acd21846" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusDomain_0a179b97-0749-49e2-adba-4ee3acd21846_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_GranteeStatusAxis_0a179b97-0749-49e2-adba-4ee3acd21846" xlink:to="loc_us-gaap_GranteeStatusDomain_0a179b97-0749-49e2-adba-4ee3acd21846_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_GranteeStatusDomain_d11049be-9800-47bd-bc84-45a40e8aae66" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_GranteeStatusDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_GranteeStatusAxis_0a179b97-0749-49e2-adba-4ee3acd21846" xlink:to="loc_us-gaap_GranteeStatusDomain_d11049be-9800-47bd-bc84-45a40e8aae66" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_693b7bf7-f627-4a00-8381-401eda8ba486" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedPaymentArrangementNonemployeeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_GranteeStatusDomain_d11049be-9800-47bd-bc84-45a40e8aae66" xlink:to="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember_693b7bf7-f627-4a00-8381-401eda8ba486" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1_ab411b29-e153-44b6-ad61-f6b782c0f4c9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_28656564-14ec-4b8f-a90b-1643771ab85c" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1_ab411b29-e153-44b6-ad61-f6b782c0f4c9" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate_56e5eb20-bf6b-4a84-83bf-50bac251c0ed" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_28656564-14ec-4b8f-a90b-1643771ab85c" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate_56e5eb20-bf6b-4a84-83bf-50bac251c0ed" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate_363eefba-319a-492b-b65d-a9c793b11a16" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_28656564-14ec-4b8f-a90b-1643771ab85c" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate_363eefba-319a-492b-b65d-a9c793b11a16" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate_f34b3419-a32f-414f-bd49-aa88d10288b3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_28656564-14ec-4b8f-a90b-1643771ab85c" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate_f34b3419-a32f-414f-bd49-aa88d10288b3" xlink:type="arc" order="3"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/StockbasedCompensationAwardActivityDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#StockbasedCompensationAwardActivityDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/StockbasedCompensationAwardActivityDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_4a1deabf-97bd-46ec-800e-6f057ae316b7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_d27da8fc-8e2d-4660-877f-d6854bbaa611" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_4a1deabf-97bd-46ec-800e-6f057ae316b7" xlink:to="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_d27da8fc-8e2d-4660-877f-d6854bbaa611" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AwardTypeAxis_dd387b19-f65a-43a7-addd-bc171e4567f1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AwardTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_d27da8fc-8e2d-4660-877f-d6854bbaa611" xlink:to="loc_us-gaap_AwardTypeAxis_dd387b19-f65a-43a7-addd-bc171e4567f1" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd387b19-f65a-43a7-addd-bc171e4567f1_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AwardTypeAxis_dd387b19-f65a-43a7-addd-bc171e4567f1" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_dd387b19-f65a-43a7-addd-bc171e4567f1_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2dc5b4d8-9d66-44e4-b531-de7e9d38b342" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AwardTypeAxis_dd387b19-f65a-43a7-addd-bc171e4567f1" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2dc5b4d8-9d66-44e4-b531-de7e9d38b342" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedStockMember_cb305a8d-5ef8-407c-a496-57e3f51de706" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2dc5b4d8-9d66-44e4-b531-de7e9d38b342" xlink:to="loc_us-gaap_RestrictedStockMember_cb305a8d-5ef8-407c-a496-57e3f51de706" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedStockUnitsRSUMember_3bd2e8e3-d46f-483e-a609-7be8e0f9ffed" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedStockUnitsRSUMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2dc5b4d8-9d66-44e4-b531-de7e9d38b342" xlink:to="loc_us-gaap_RestrictedStockUnitsRSUMember_3bd2e8e3-d46f-483e-a609-7be8e0f9ffed" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceStockUnitsMember_5f174c87-8a39-4377-b4e1-0be58b9556db" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceStockUnitsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2dc5b4d8-9d66-44e4-b531-de7e9d38b342" xlink:to="loc_cdxs_PerformanceStockUnitsMember_5f174c87-8a39-4377-b4e1-0be58b9556db" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceBasedOptionsPBOsMember_7e0368a7-fa50-4b2b-b50a-4c90899953d4" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceBasedOptionsPBOsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2dc5b4d8-9d66-44e4-b531-de7e9d38b342" xlink:to="loc_cdxs_PerformanceBasedOptionsPBOsMember_7e0368a7-fa50-4b2b-b50a-4c90899953d4" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PerformanceSharesMember_cb71ebf3-bb29-4489-9e5a-16fe43983f31" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PerformanceSharesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2dc5b4d8-9d66-44e4-b531-de7e9d38b342" xlink:to="loc_us-gaap_PerformanceSharesMember_cb71ebf3-bb29-4489-9e5a-16fe43983f31" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_4a1deabf-97bd-46ec-800e-6f057ae316b7" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber_44a9d9c9-7f3a-49db-b845-aca54dc42a3a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber_44a9d9c9-7f3a-49db-b845-aca54dc42a3a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod_169395dd-a314-49a5-a94c-9cbd9b866826" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod_169395dd-a314-49a5-a94c-9cbd9b866826" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod_f408272d-a4b4-4df7-9b18-71fdaf504eab" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod_f408272d-a4b4-4df7-9b18-71fdaf504eab" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNonOptionEquityInstrumentsExercised_46acd06e-1dd0-410e-8e9d-a512f8cffd2c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNonOptionEquityInstrumentsExercised"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNonOptionEquityInstrumentsExercised_46acd06e-1dd0-410e-8e9d-a512f8cffd2c" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod_155530c2-463f-4cc3-a134-359defb4c7b6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod_155530c2-463f-4cc3-a134-359defb4c7b6" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOtherInPeriod_9fa875f5-c1db-4a9a-a8bf-ad0b858f050e" xlink:href="cdxs-20231231.xsd#cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOtherInPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedRollForward_ad7a4e8f-58b5-4c03-bb95-0e3951561a84" xlink:to="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOtherInPeriod_9fa875f5-c1db-4a9a-a8bf-ad0b858f050e" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber_dbbca502-7cc3-4ffa-a53a-9d44e8d459ee" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_4a1deabf-97bd-46ec-800e-6f057ae316b7" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue_8cbcd7ce-6a12-40fe-9bb1-7ead2c290f10" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue_8cbcd7ce-6a12-40fe-9bb1-7ead2c290f10" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue_4def8abe-0d5f-4c03-9837-63b1945e2896" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue_4def8abe-0d5f-4c03-9837-63b1945e2896" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue_42bc7268-0605-4db8-9a37-bcf33aa10be7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue_42bc7268-0605-4db8-9a37-bcf33aa10be7" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardNonOptionEquityInstrumentsExercisedWeightedAverageGrantDateFairValue_9f6e4691-fe6b-4497-bc03-e27e875dbcd7" xlink:href="cdxs-20231231.xsd#cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardNonOptionEquityInstrumentsExercisedWeightedAverageGrantDateFairValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:to="loc_cdxs_SharebasedCompensationArrangementbySharebasedPaymentAwardNonOptionEquityInstrumentsExercisedWeightedAverageGrantDateFairValue_9f6e4691-fe6b-4497-bc03-e27e875dbcd7" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue_9b9804fa-3abd-40da-9bfa-11dc9702afa3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue_9b9804fa-3abd-40da-9bfa-11dc9702afa3" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOtherInPeriodWeightedAverageGrantDateFairValue_943feea1-4d89-4701-b7ad-ad0c3f53147b" xlink:href="cdxs-20231231.xsd#cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOtherInPeriodWeightedAverageGrantDateFairValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValueRollForward_7de1ae9c-a77f-4fc2-9474-650765391287" xlink:to="loc_cdxs_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOtherInPeriodWeightedAverageGrantDateFairValue_943feea1-4d89-4701-b7ad-ad0c3f53147b" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue_d8d06eeb-17d1-4f43-a00b-109707ee1492" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_4a1deabf-97bd-46ec-800e-6f057ae316b7" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber_7ad7eb47-bc42-4ec6-81d7-d454601bb23b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber_7ad7eb47-bc42-4ec6-81d7-d454601bb23b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber_d0c12252-322b-4a50-8b6f-1460da298e75" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber_d0c12252-322b-4a50-8b6f-1460da298e75" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice_9adb3596-a454-476b-b358-ccaa2acb5cb6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice_9adb3596-a454-476b-b358-ccaa2acb5cb6" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice_436dc5a0-6210-4923-9369-add6150468c5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice_436dc5a0-6210-4923-9369-add6150468c5" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1_cfdafb74-e6ee-4e01-ac03-fd3e6acb64c5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1_cfdafb74-e6ee-4e01-ac03-fd3e6acb64c5" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1_67c2e529-74d8-47bb-8397-02f3678a66f9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1_67c2e529-74d8-47bb-8397-02f3678a66f9" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1_c4e7570b-7f88-4e67-b096-20c41ada66b7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1_c4e7570b-7f88-4e67-b096-20c41ada66b7" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue_cabd037e-1e54-4269-90f1-60606c3a555e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestAbstract_ca31debd-c76f-493d-8c1c-14374dfeff6d" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue_cabd037e-1e54-4269-90f1-60606c3a555e" xlink:type="arc" order="8"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CapitalStockDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CapitalStockDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CapitalStockDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfStockByClassTable_8a03dd99-1093-44b9-9ef8-0725c9d0e5d6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfStockByClassTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_us-gaap_ScheduleOfStockByClassTable_8a03dd99-1093-44b9-9ef8-0725c9d0e5d6" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_dei_LegalEntityAxis_925dce7e-1cc4-427f-b4f8-40cb893bac1c" xlink:href="https://xbrl.sec.gov/dei/2023/dei-2023.xsd#dei_LegalEntityAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfStockByClassTable_8a03dd99-1093-44b9-9ef8-0725c9d0e5d6" xlink:to="loc_dei_LegalEntityAxis_925dce7e-1cc4-427f-b4f8-40cb893bac1c" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_dei_EntityDomain_925dce7e-1cc4-427f-b4f8-40cb893bac1c_default" xlink:href="https://xbrl.sec.gov/dei/2023/dei-2023.xsd#dei_EntityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_dei_LegalEntityAxis_925dce7e-1cc4-427f-b4f8-40cb893bac1c" xlink:to="loc_dei_EntityDomain_925dce7e-1cc4-427f-b4f8-40cb893bac1c_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_dei_EntityDomain_dd8b5f7e-b097-45f1-9679-e37405935c4f" xlink:href="https://xbrl.sec.gov/dei/2023/dei-2023.xsd#dei_EntityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_dei_LegalEntityAxis_925dce7e-1cc4-427f-b4f8-40cb893bac1c" xlink:to="loc_dei_EntityDomain_dd8b5f7e-b097-45f1-9679-e37405935c4f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PiperSandlerCoMember_17183159-14a6-4def-998a-0f1583b0f49d" xlink:href="cdxs-20231231.xsd#cdxs_PiperSandlerCoMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_dei_EntityDomain_dd8b5f7e-b097-45f1-9679-e37405935c4f" xlink:to="loc_cdxs_PiperSandlerCoMember_17183159-14a6-4def-998a-0f1583b0f49d" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeAxis_fa9e4b7a-7caa-4598-8a32-fe6e0a36f96f" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfStockByClassTable_8a03dd99-1093-44b9-9ef8-0725c9d0e5d6" xlink:to="loc_srt_RangeAxis_fa9e4b7a-7caa-4598-8a32-fe6e0a36f96f" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_fa9e4b7a-7caa-4598-8a32-fe6e0a36f96f_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_RangeAxis_fa9e4b7a-7caa-4598-8a32-fe6e0a36f96f" xlink:to="loc_srt_RangeMember_fa9e4b7a-7caa-4598-8a32-fe6e0a36f96f_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_8902ec55-7f66-4612-945f-4ec6cfa5af70" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RangeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_RangeAxis_fa9e4b7a-7caa-4598-8a32-fe6e0a36f96f" xlink:to="loc_srt_RangeMember_8902ec55-7f66-4612-945f-4ec6cfa5af70" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_MaximumMember_d4264249-7af0-40d6-910b-4bb79a516757" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_MaximumMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RangeMember_8902ec55-7f66-4612-945f-4ec6cfa5af70" xlink:to="loc_srt_MaximumMember_d4264249-7af0-40d6-910b-4bb79a516757" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockSecuritiesRegisteredAggregateAmount_00bf2a22-25b6-438c-aca6-3a70f235602f" xlink:href="cdxs-20231231.xsd#cdxs_SaleOfStockSecuritiesRegisteredAggregateAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_cdxs_SaleOfStockSecuritiesRegisteredAggregateAmount_00bf2a22-25b6-438c-aca6-3a70f235602f" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockPeriod_8c25d1cb-3dd0-445d-8f8f-bfcd7ca2d69d" xlink:href="cdxs-20231231.xsd#cdxs_SaleOfStockPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_cdxs_SaleOfStockPeriod_8c25d1cb-3dd0-445d-8f8f-bfcd7ca2d69d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockValueOfSharesForIssuance_90d7669b-8fb5-498a-9349-1c0cc1150a2b" xlink:href="cdxs-20231231.xsd#cdxs_SaleOfStockValueOfSharesForIssuance"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_cdxs_SaleOfStockValueOfSharesForIssuance_90d7669b-8fb5-498a-9349-1c0cc1150a2b" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockCommissionsPercentageOfGrossSalesPrice_d0de9f65-cc29-4b6c-aa49-3271cadeacd2" xlink:href="cdxs-20231231.xsd#cdxs_SaleOfStockCommissionsPercentageOfGrossSalesPrice"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_cdxs_SaleOfStockCommissionsPercentageOfGrossSalesPrice_d0de9f65-cc29-4b6c-aa49-3271cadeacd2" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockCommissionsAndReimbursementsPercentageOfGrossSalesPrice_133d626f-463d-42fb-837f-524fb012db30" xlink:href="cdxs-20231231.xsd#cdxs_SaleOfStockCommissionsAndReimbursementsPercentageOfGrossSalesPrice"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_cdxs_SaleOfStockCommissionsAndReimbursementsPercentageOfGrossSalesPrice_133d626f-463d-42fb-837f-524fb012db30" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_c3a679ec-c88c-4495-8cf6-c5665da1a0c5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_c3a679ec-c88c-4495-8cf6-c5665da1a0c5" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockConsiderationReceivedOnTransactionGross_fc326a94-88f1-497b-ade8-6491609b8aad" xlink:href="cdxs-20231231.xsd#cdxs_SaleOfStockConsiderationReceivedOnTransactionGross"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_cdxs_SaleOfStockConsiderationReceivedOnTransactionGross_fc326a94-88f1-497b-ade8-6491609b8aad" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockConsiderationReceivedOnTransaction_1b554b09-155c-42b5-9e62-31010e37bb58" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SaleOfStockConsiderationReceivedOnTransaction"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_us-gaap_SaleOfStockConsiderationReceivedOnTransaction_1b554b09-155c-42b5-9e62-31010e37bb58" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsOfStockIssuanceCosts_8b6195ae-61fd-407b-adad-e8ee084c87c3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PaymentsOfStockIssuanceCosts"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_e5a45d81-629c-4e2e-b48e-48dec35c0605" xlink:to="loc_us-gaap_PaymentsOfStockIssuanceCosts_8b6195ae-61fd-407b-adad-e8ee084c87c3" xlink:type="arc" order="8"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/IncomeTaxesNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#IncomeTaxesNarrativeDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/IncomeTaxesNarrativeDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ValuationAllowanceLineItems_3d660a0f-1fff-4a8f-88e1-061e4dcb652f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ValuationAllowanceLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ValuationAllowanceTable_e231018b-11b7-4755-9f30-48b93e0e676d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ValuationAllowanceTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ValuationAllowanceLineItems_3d660a0f-1fff-4a8f-88e1-061e4dcb652f" xlink:to="loc_us-gaap_ValuationAllowanceTable_e231018b-11b7-4755-9f30-48b93e0e676d" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_StatementGeographicalAxis_e128187f-1863-4c95-91df-49982b966e21" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_StatementGeographicalAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ValuationAllowanceTable_e231018b-11b7-4755-9f30-48b93e0e676d" xlink:to="loc_srt_StatementGeographicalAxis_e128187f-1863-4c95-91df-49982b966e21" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_e128187f-1863-4c95-91df-49982b966e21_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_SegmentGeographicalDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_StatementGeographicalAxis_e128187f-1863-4c95-91df-49982b966e21" xlink:to="loc_srt_SegmentGeographicalDomain_e128187f-1863-4c95-91df-49982b966e21_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_a68046f6-95be-4a2e-bc29-020b24139e81" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_SegmentGeographicalDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_StatementGeographicalAxis_e128187f-1863-4c95-91df-49982b966e21" xlink:to="loc_srt_SegmentGeographicalDomain_a68046f6-95be-4a2e-bc29-020b24139e81" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_country_IN_0e803642-4fa3-4606-97d4-b2633e63e294" xlink:href="https://xbrl.sec.gov/country/2023/country-2023.xsd#country_IN"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_a68046f6-95be-4a2e-bc29-020b24139e81" xlink:to="loc_country_IN_0e803642-4fa3-4606-97d4-b2633e63e294" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ValuationAllowanceDeferredTaxAssetChangeInAmount_37c77624-e29d-4e77-a6f5-b35b8ded4bf0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ValuationAllowanceDeferredTaxAssetChangeInAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ValuationAllowanceLineItems_3d660a0f-1fff-4a8f-88e1-061e4dcb652f" xlink:to="loc_us-gaap_ValuationAllowanceDeferredTaxAssetChangeInAmount_37c77624-e29d-4e77-a6f5-b35b8ded4bf0" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DeferredTaxLiabilitiesUndistributedForeignEarnings_1cec56c7-a048-4542-ac1e-16287d5f6809" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DeferredTaxLiabilitiesUndistributedForeignEarnings"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ValuationAllowanceLineItems_3d660a0f-1fff-4a8f-88e1-061e4dcb652f" xlink:to="loc_us-gaap_DeferredTaxLiabilitiesUndistributedForeignEarnings_1cec56c7-a048-4542-ac1e-16287d5f6809" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_UnrecognizedTaxBenefitsIncomeTaxPenaltiesAndInterestExpense_4ffdece0-e4f5-4db6-9b1a-c93d4238ebf4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_UnrecognizedTaxBenefitsIncomeTaxPenaltiesAndInterestExpense"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ValuationAllowanceLineItems_3d660a0f-1fff-4a8f-88e1-061e4dcb652f" xlink:to="loc_us-gaap_UnrecognizedTaxBenefitsIncomeTaxPenaltiesAndInterestExpense_4ffdece0-e4f5-4db6-9b1a-c93d4238ebf4" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_UnrecognizedTaxBenefitsIncomeTaxPenaltiesAndInterestAccrued_5a4cab13-53ad-4b94-95a1-ed073d121bee" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_UnrecognizedTaxBenefitsIncomeTaxPenaltiesAndInterestAccrued"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ValuationAllowanceLineItems_3d660a0f-1fff-4a8f-88e1-061e4dcb652f" xlink:to="loc_us-gaap_UnrecognizedTaxBenefitsIncomeTaxPenaltiesAndInterestAccrued_5a4cab13-53ad-4b94-95a1-ed073d121bee" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_UnrecognizedTaxBenefitsThatWouldImpactEffectiveTaxRate_4d3f5ed8-975c-4d68-9ae0-1be0083fe5c9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_UnrecognizedTaxBenefitsThatWouldImpactEffectiveTaxRate"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ValuationAllowanceLineItems_3d660a0f-1fff-4a8f-88e1-061e4dcb652f" xlink:to="loc_us-gaap_UnrecognizedTaxBenefitsThatWouldImpactEffectiveTaxRate_4d3f5ed8-975c-4d68-9ae0-1be0083fe5c9" xlink:type="arc" order="4"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/IncomeTaxesNOLCarryforwardsandFederalResearchandDevelopmentTaxCreditsDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#IncomeTaxesNOLCarryforwardsandFederalResearchandDevelopmentTaxCreditsDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/IncomeTaxesNOLCarryforwardsandFederalResearchandDevelopmentTaxCreditsDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsLineItems_89bd51b4-4965-4f55-a8c7-5e1c053e01ec" xlink:href="cdxs-20231231.xsd#cdxs_OperatingLossAndTaxCreditCarryforwardsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsTable_4392a421-0378-4e78-b293-d302b0a1dcd2" xlink:href="cdxs-20231231.xsd#cdxs_OperatingLossAndTaxCreditCarryforwardsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsLineItems_89bd51b4-4965-4f55-a8c7-5e1c053e01ec" xlink:to="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsTable_4392a421-0378-4e78-b293-d302b0a1dcd2" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeTaxAuthorityAxis_764d8f07-d9a7-4299-9a9d-e32c878c950d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeTaxAuthorityAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsTable_4392a421-0378-4e78-b293-d302b0a1dcd2" xlink:to="loc_us-gaap_IncomeTaxAuthorityAxis_764d8f07-d9a7-4299-9a9d-e32c878c950d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeTaxAuthorityDomain_764d8f07-d9a7-4299-9a9d-e32c878c950d_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeTaxAuthorityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_IncomeTaxAuthorityAxis_764d8f07-d9a7-4299-9a9d-e32c878c950d" xlink:to="loc_us-gaap_IncomeTaxAuthorityDomain_764d8f07-d9a7-4299-9a9d-e32c878c950d_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeTaxAuthorityDomain_0eda8d89-549d-4e28-9084-a6990858e384" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IncomeTaxAuthorityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_IncomeTaxAuthorityAxis_764d8f07-d9a7-4299-9a9d-e32c878c950d" xlink:to="loc_us-gaap_IncomeTaxAuthorityDomain_0eda8d89-549d-4e28-9084-a6990858e384" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DomesticCountryMember_bae8bbc3-8680-4a2c-bb04-b3e8befb9ba6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DomesticCountryMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncomeTaxAuthorityDomain_0eda8d89-549d-4e28-9084-a6990858e384" xlink:to="loc_us-gaap_DomesticCountryMember_bae8bbc3-8680-4a2c-bb04-b3e8befb9ba6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StateAndLocalJurisdictionMember_9e7e0bcf-54a7-4115-a4f4-4a9f11319f22" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StateAndLocalJurisdictionMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncomeTaxAuthorityDomain_0eda8d89-549d-4e28-9084-a6990858e384" xlink:to="loc_us-gaap_StateAndLocalJurisdictionMember_9e7e0bcf-54a7-4115-a4f4-4a9f11319f22" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLossCarryforwards_ecd10a76-d29f-46fc-9fe1-c5c15e6487a5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OperatingLossCarryforwards"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsLineItems_89bd51b4-4965-4f55-a8c7-5e1c053e01ec" xlink:to="loc_us-gaap_OperatingLossCarryforwards_ecd10a76-d29f-46fc-9fe1-c5c15e6487a5" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DeferredTaxAssetsOperatingLossCarryforwardsNotSubjectToExpiration_693d2cda-8470-4b6f-a31e-f4aeb553dcc3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DeferredTaxAssetsOperatingLossCarryforwardsNotSubjectToExpiration"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsLineItems_89bd51b4-4965-4f55-a8c7-5e1c053e01ec" xlink:to="loc_us-gaap_DeferredTaxAssetsOperatingLossCarryforwardsNotSubjectToExpiration_693d2cda-8470-4b6f-a31e-f4aeb553dcc3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TaxCreditCarryforwardAmount_dab24eb4-bcd8-45e4-95b6-4473bd1d05e7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TaxCreditCarryforwardAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_cdxs_OperatingLossAndTaxCreditCarryforwardsLineItems_89bd51b4-4965-4f55-a8c7-5e1c053e01ec" xlink:to="loc_us-gaap_TaxCreditCarryforwardAmount_dab24eb4-bcd8-45e4-95b6-4473bd1d05e7" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CommitmentsandContingenciesNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CommitmentsandContingenciesNarrativeDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CommitmentsandContingenciesNarrativeDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LongTermPurchaseCommitmentLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LongTermPurchaseCommitmentTable_e5fa10d6-2f03-439a-932e-51744cabeff4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LongTermPurchaseCommitmentTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_LongTermPurchaseCommitmentTable_e5fa10d6-2f03-439a-932e-51744cabeff4" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_53a72cc7-3bcf-4996-a101-2da42555830b" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentTable_e5fa10d6-2f03-439a-932e-51744cabeff4" xlink:to="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_53a72cc7-3bcf-4996-a101-2da42555830b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_53a72cc7-3bcf-4996-a101-2da42555830b_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_53a72cc7-3bcf-4996-a101-2da42555830b" xlink:to="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_53a72cc7-3bcf-4996-a101-2da42555830b_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_afdf5f29-2e7f-47e2-8d9e-8c0e8a3736e8" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationDescriptionOfPropertyAxis_53a72cc7-3bcf-4996-a101-2da42555830b" xlink:to="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_afdf5f29-2e7f-47e2-8d9e-8c0e8a3736e8" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A200220PenobscotMember_2b58d5b6-635e-4722-907b-3bb67510c3df" xlink:href="cdxs-20231231.xsd#cdxs_A200220PenobscotMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_afdf5f29-2e7f-47e2-8d9e-8c0e8a3736e8" xlink:to="loc_cdxs_A200220PenobscotMember_2b58d5b6-635e-4722-907b-3bb67510c3df" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A400PenoscotMember_5439ddbe-740b-4004-afb2-605bcfd8544f" xlink:href="cdxs-20231231.xsd#cdxs_A400PenoscotMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_afdf5f29-2e7f-47e2-8d9e-8c0e8a3736e8" xlink:to="loc_cdxs_A400PenoscotMember_5439ddbe-740b-4004-afb2-605bcfd8544f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_A501ChesapeakeMember_b9914cf3-dc77-40f3-9bb3-5161242310db" xlink:href="cdxs-20231231.xsd#cdxs_A501ChesapeakeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_afdf5f29-2e7f-47e2-8d9e-8c0e8a3736e8" xlink:to="loc_cdxs_A501ChesapeakeMember_b9914cf3-dc77-40f3-9bb3-5161242310db" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_SanCarlosMember_05226d2e-8236-4858-98bd-f4dcaf609131" xlink:href="cdxs-20231231.xsd#cdxs_SanCarlosMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RealEstateAndAccumulatedDepreciationNameOfPropertyDomain_afdf5f29-2e7f-47e2-8d9e-8c0e8a3736e8" xlink:to="loc_cdxs_SanCarlosMember_05226d2e-8236-4858-98bd-f4dcaf609131" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_3b452894-5dc8-4ae4-b689-3898f4d60139" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentTable_e5fa10d6-2f03-439a-932e-51744cabeff4" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_3b452894-5dc8-4ae4-b689-3898f4d60139" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_3b452894-5dc8-4ae4-b689-3898f4d60139_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_3b452894-5dc8-4ae4-b689-3898f4d60139" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_3b452894-5dc8-4ae4-b689-3898f4d60139_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_3cbae42d-7491-4f68-901b-ba53cfa77979" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsAxis_3b452894-5dc8-4ae4-b689-3898f4d60139" xlink:to="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_3cbae42d-7491-4f68-901b-ba53cfa77979" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DemandDepositsMember_42e7f9f2-e969-4822-a8e7-eeb1d99f3735" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DemandDepositsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_3cbae42d-7491-4f68-901b-ba53cfa77979" xlink:to="loc_us-gaap_DemandDepositsMember_42e7f9f2-e969-4822-a8e7-eeb1d99f3735" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CreditFacilityAxis_d4a2eefc-5ce9-47ef-83e7-a50d43deff31" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CreditFacilityAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentTable_e5fa10d6-2f03-439a-932e-51744cabeff4" xlink:to="loc_us-gaap_CreditFacilityAxis_d4a2eefc-5ce9-47ef-83e7-a50d43deff31" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CreditFacilityDomain_d4a2eefc-5ce9-47ef-83e7-a50d43deff31_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CreditFacilityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_CreditFacilityAxis_d4a2eefc-5ce9-47ef-83e7-a50d43deff31" xlink:to="loc_us-gaap_CreditFacilityDomain_d4a2eefc-5ce9-47ef-83e7-a50d43deff31_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CreditFacilityDomain_4671ac64-196e-4698-9601-b5411205be03" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CreditFacilityDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_CreditFacilityAxis_d4a2eefc-5ce9-47ef-83e7-a50d43deff31" xlink:to="loc_us-gaap_CreditFacilityDomain_4671ac64-196e-4698-9601-b5411205be03" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TermLoanMember_c0d1665d-59ce-49c9-b52e-768e217fa360" xlink:href="cdxs-20231231.xsd#cdxs_TermLoanMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CreditFacilityDomain_4671ac64-196e-4698-9601-b5411205be03" xlink:to="loc_cdxs_TermLoanMember_c0d1665d-59ce-49c9-b52e-768e217fa360" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevolvingCreditFacilityMember_37823197-5ed3-42ba-9cc1-4bb6daa7cc9f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevolvingCreditFacilityMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_CreditFacilityDomain_4671ac64-196e-4698-9601-b5411205be03" xlink:to="loc_us-gaap_RevolvingCreditFacilityMember_37823197-5ed3-42ba-9cc1-4bb6daa7cc9f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_03258756-7390-42d0-b963-535f7e10b9bc" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LossContingenciesByNatureOfContingencyAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentTable_e5fa10d6-2f03-439a-932e-51744cabeff4" xlink:to="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_03258756-7390-42d0-b963-535f7e10b9bc" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingencyNatureDomain_03258756-7390-42d0-b963-535f7e10b9bc_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LossContingencyNatureDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_03258756-7390-42d0-b963-535f7e10b9bc" xlink:to="loc_us-gaap_LossContingencyNatureDomain_03258756-7390-42d0-b963-535f7e10b9bc_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingencyNatureDomain_aa7ea785-8c40-4ba4-b4a4-1cdcbb3f6fa3" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LossContingencyNatureDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_03258756-7390-42d0-b963-535f7e10b9bc" xlink:to="loc_us-gaap_LossContingencyNatureDomain_aa7ea785-8c40-4ba4-b4a4-1cdcbb3f6fa3" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_IndemnificationGuaranteeMember_b282a205-aa15-4609-9c34-00bdf3d97c09" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_IndemnificationGuaranteeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LossContingencyNatureDomain_aa7ea785-8c40-4ba4-b4a4-1cdcbb3f6fa3" xlink:to="loc_us-gaap_IndemnificationGuaranteeMember_b282a205-aa15-4609-9c34-00bdf3d97c09" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AreaOfRealEstateProperty_51508d37-0ae3-4311-a9fb-0f2945ba545b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AreaOfRealEstateProperty"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_AreaOfRealEstateProperty_51508d37-0ae3-4311-a9fb-0f2945ba545b" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_LesseeOperatingLeaseOptionToExtendNumber_a29804b2-4222-4e5a-8b4d-23077c08681f" xlink:href="cdxs-20231231.xsd#cdxs_LesseeOperatingLeaseOptionToExtendNumber"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_cdxs_LesseeOperatingLeaseOptionToExtendNumber_a29804b2-4222-4e5a-8b4d-23077c08681f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseRenewalTerm_89b17b57-576e-4ad8-b0b9-dc40c8573def" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LesseeOperatingLeaseRenewalTerm"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_LesseeOperatingLeaseRenewalTerm_89b17b57-576e-4ad8-b0b9-dc40c8573def" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashAndInvestmentsNoncurrent_fad80c75-2d2b-4491-a1af-7956bf547a86" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedCashAndInvestmentsNoncurrent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_RestrictedCashAndInvestmentsNoncurrent_fad80c75-2d2b-4491-a1af-7956bf547a86" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLeaseNotYetCommencedTermOfContract1_01b7c449-05d2-4611-bbd7-0b5ab52a0d83" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LesseeOperatingLeaseLeaseNotYetCommencedTermOfContract1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_LesseeOperatingLeaseLeaseNotYetCommencedTermOfContract1_01b7c449-05d2-4611-bbd7-0b5ab52a0d83" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLeaseNotYetCommencedRenewalTerm1_3ac633db-11a4-40e5-aae2-1436f6f768c2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LesseeOperatingLeaseLeaseNotYetCommencedRenewalTerm1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_LesseeOperatingLeaseLeaseNotYetCommencedRenewalTerm1_3ac633db-11a4-40e5-aae2-1436f6f768c2" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLeaseLiability_36975025-454b-41f0-9374-082c0d83a628" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OperatingLeaseLiability"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_OperatingLeaseLiability_36975025-454b-41f0-9374-082c0d83a628" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityDeposit_de29fbf8-31a6-415e-8d58-817832121635" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SecurityDeposit"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_SecurityDeposit_de29fbf8-31a6-415e-8d58-817832121635" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_OperatingLeaseWriteOffDueToLeaseModification_bbdba97c-e633-425e-ad4b-9bd8f723bbfc" xlink:href="cdxs-20231231.xsd#cdxs_OperatingLeaseWriteOffDueToLeaseModification"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_cdxs_OperatingLeaseWriteOffDueToLeaseModification_bbdba97c-e633-425e-ad4b-9bd8f723bbfc" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AssetImpairmentCharges_5436fc03-812b-4b25-8dd8-b742eeb2ba87" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AssetImpairmentCharges"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_AssetImpairmentCharges_5436fc03-812b-4b25-8dd8-b742eeb2ba87" xlink:type="arc" order="9"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ImpairmentOfLeasehold_375f9641-0935-4e7a-aeb4-3613cf5db61a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ImpairmentOfLeasehold"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_ImpairmentOfLeasehold_375f9641-0935-4e7a-aeb4-3613cf5db61a" xlink:type="arc" order="10"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLeaseImpairmentLoss_27e0c78c-25b7-4ef3-a20d-9d52a1637db7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OperatingLeaseImpairmentLoss"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_OperatingLeaseImpairmentLoss_27e0c78c-25b7-4ef3-a20d-9d52a1637db7" xlink:type="arc" order="11"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_AssetRetirementObligationWriteoff_b051e154-d917-4bd4-a648-9c27981e909d" xlink:href="cdxs-20231231.xsd#cdxs_AssetRetirementObligationWriteoff"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_cdxs_AssetRetirementObligationWriteoff_b051e154-d917-4bd4-a648-9c27981e909d" xlink:type="arc" order="12"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AssetRetirementObligation_091dd62c-af14-45c7-ad89-84d18eac0cb4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AssetRetirementObligation"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_AssetRetirementObligation_091dd62c-af14-45c7-ad89-84d18eac0cb4" xlink:type="arc" order="13"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LineOfCreditFacilityCurrentBorrowingCapacity_6aefd6ec-ba48-4508-917e-972792374b37" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LineOfCreditFacilityCurrentBorrowingCapacity"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_LineOfCreditFacilityCurrentBorrowingCapacity_6aefd6ec-ba48-4508-917e-972792374b37" xlink:type="arc" order="14"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_LineOfCreditFacilityAccountsReceivableBorrowingBasePercentage_71bbda13-a6f6-40ae-9106-6ee58eee0620" xlink:href="cdxs-20231231.xsd#cdxs_LineOfCreditFacilityAccountsReceivableBorrowingBasePercentage"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_cdxs_LineOfCreditFacilityAccountsReceivableBorrowingBasePercentage_71bbda13-a6f6-40ae-9106-6ee58eee0620" xlink:type="arc" order="15"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingencyAccrualCarryingValueCurrent_f0efec97-66b7-4877-9c8c-317fc1436297" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LossContingencyAccrualCarryingValueCurrent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongTermPurchaseCommitmentLineItems_c261fd9e-1292-4485-bb3f-f1867bb0e2b5" xlink:to="loc_us-gaap_LossContingencyAccrualCarryingValueCurrent_f0efec97-66b7-4877-9c8c-317fc1436297" xlink:type="arc" order="16"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/CommitmentsandContingenciesOtherCommitmentsDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#CommitmentsandContingenciesOtherCommitmentsDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/CommitmentsandContingenciesOtherCommitmentsDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentsLineItems_4056c2a3-c6d5-41c4-b32e-b4c67cb4e182" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherCommitmentsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingenciesTable_5b21460b-44cd-43e3-9398-928c718c30da" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_LossContingenciesTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_OtherCommitmentsLineItems_4056c2a3-c6d5-41c4-b32e-b4c67cb4e182" xlink:to="loc_us-gaap_LossContingenciesTable_5b21460b-44cd-43e3-9398-928c718c30da" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentsAxis_fb685f9b-c83a-45f4-a542-5e6da0637029" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherCommitmentsAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_LossContingenciesTable_5b21460b-44cd-43e3-9398-928c718c30da" xlink:to="loc_us-gaap_OtherCommitmentsAxis_fb685f9b-c83a-45f4-a542-5e6da0637029" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentsDomain_fb685f9b-c83a-45f4-a542-5e6da0637029_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherCommitmentsDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_OtherCommitmentsAxis_fb685f9b-c83a-45f4-a542-5e6da0637029" xlink:to="loc_us-gaap_OtherCommitmentsDomain_fb685f9b-c83a-45f4-a542-5e6da0637029_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentsDomain_16276bcd-3114-45a6-a2bf-8b4f336700c5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherCommitmentsDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_OtherCommitmentsAxis_fb685f9b-c83a-45f4-a542-5e6da0637029" xlink:to="loc_us-gaap_OtherCommitmentsDomain_16276bcd-3114-45a6-a2bf-8b4f336700c5" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_FacilityMaintenanceAgreementMember_958bf611-27ed-4d1f-8a72-2b3f7b707222" xlink:href="cdxs-20231231.xsd#cdxs_FacilityMaintenanceAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OtherCommitmentsDomain_16276bcd-3114-45a6-a2bf-8b4f336700c5" xlink:to="loc_cdxs_FacilityMaintenanceAgreementMember_958bf611-27ed-4d1f-8a72-2b3f7b707222" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitment_acd74c8a-bf5b-4333-981b-6b6c8dd6421d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherCommitment"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OtherCommitmentsLineItems_4056c2a3-c6d5-41c4-b32e-b4c67cb4e182" xlink:to="loc_us-gaap_OtherCommitment_acd74c8a-bf5b-4333-981b-6b6c8dd6421d" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentDueInNextTwelveMonths_07d223f5-c0c4-4e89-9118-bf32e11a6230" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherCommitmentDueInNextTwelveMonths"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OtherCommitmentsLineItems_4056c2a3-c6d5-41c4-b32e-b4c67cb4e182" xlink:to="loc_us-gaap_OtherCommitmentDueInNextTwelveMonths_07d223f5-c0c4-4e89-9118-bf32e11a6230" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentDueInSecondYear_c0d6b3cf-9f5a-4be8-9057-2b6082d59006" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OtherCommitmentDueInSecondYear"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OtherCommitmentsLineItems_4056c2a3-c6d5-41c4-b32e-b4c67cb4e182" xlink:to="loc_us-gaap_OtherCommitmentDueInSecondYear_c0d6b3cf-9f5a-4be8-9057-2b6082d59006" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/RelatedPartyTransactionsDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#RelatedPartyTransactionsDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/RelatedPartyTransactionsDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionLineItems_cf49ab96-f622-4f66-a0bd-90bbb0a7f962" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable_ae8ec08c-0a05-40d0-a759-1458192e795a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_RelatedPartyTransactionLineItems_cf49ab96-f622-4f66-a0bd-90bbb0a7f962" xlink:to="loc_us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable_ae8ec08c-0a05-40d0-a759-1458192e795a" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_cb11de8e-67bb-48ef-aa95-c6c0fed3446a" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable_ae8ec08c-0a05-40d0-a759-1458192e795a" xlink:to="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_cb11de8e-67bb-48ef-aa95-c6c0fed3446a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_EquityMethodInvesteeNameDomain_cb11de8e-67bb-48ef-aa95-c6c0fed3446a_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_EquityMethodInvesteeNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_cb11de8e-67bb-48ef-aa95-c6c0fed3446a" xlink:to="loc_srt_EquityMethodInvesteeNameDomain_cb11de8e-67bb-48ef-aa95-c6c0fed3446a_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_EquityMethodInvesteeNameDomain_59b53239-4f34-42ff-a766-96c90f9aef1e" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_EquityMethodInvesteeNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ScheduleOfEquityMethodInvestmentEquityMethodInvesteeNameAxis_cb11de8e-67bb-48ef-aa95-c6c0fed3446a" xlink:to="loc_srt_EquityMethodInvesteeNameDomain_59b53239-4f34-42ff-a766-96c90f9aef1e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MolecularAssembliesIncMember_1318cbb3-815d-43fa-9363-ad99ff97a6bb" xlink:href="cdxs-20231231.xsd#cdxs_MolecularAssembliesIncMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_EquityMethodInvesteeNameDomain_59b53239-4f34-42ff-a766-96c90f9aef1e" xlink:to="loc_cdxs_MolecularAssembliesIncMember_1318cbb3-815d-43fa-9363-ad99ff97a6bb" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementClassOfStockAxis_dcaedbae-3ca2-46fd-8154-60886ab249c1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementClassOfStockAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable_ae8ec08c-0a05-40d0-a759-1458192e795a" xlink:to="loc_us-gaap_StatementClassOfStockAxis_dcaedbae-3ca2-46fd-8154-60886ab249c1" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_dcaedbae-3ca2-46fd-8154-60886ab249c1_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementClassOfStockAxis_dcaedbae-3ca2-46fd-8154-60886ab249c1" xlink:to="loc_us-gaap_ClassOfStockDomain_dcaedbae-3ca2-46fd-8154-60886ab249c1_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_ea26bbd7-5aa5-4385-846e-7e144df4f8e4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementClassOfStockAxis_dcaedbae-3ca2-46fd-8154-60886ab249c1" xlink:to="loc_us-gaap_ClassOfStockDomain_ea26bbd7-5aa5-4385-846e-7e144df4f8e4" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SeriesAPreferredStockMember_70f10911-344f-4134-8c30-d22bd90896d7" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SeriesAPreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_ea26bbd7-5aa5-4385-846e-7e144df4f8e4" xlink:to="loc_us-gaap_SeriesAPreferredStockMember_70f10911-344f-4134-8c30-d22bd90896d7" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SeriesBPreferredStockMember_7a626008-113c-410e-b290-ec0bcfa688f1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SeriesBPreferredStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_ea26bbd7-5aa5-4385-846e-7e144df4f8e4" xlink:to="loc_us-gaap_SeriesBPreferredStockMember_7a626008-113c-410e-b290-ec0bcfa688f1" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_CounterpartyNameAxis_a5ee22e2-f9ed-4c2a-baf1-6939101fdc2a" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_CounterpartyNameAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable_ae8ec08c-0a05-40d0-a759-1458192e795a" xlink:to="loc_srt_CounterpartyNameAxis_a5ee22e2-f9ed-4c2a-baf1-6939101fdc2a" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_a5ee22e2-f9ed-4c2a-baf1-6939101fdc2a_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_CounterpartyNameAxis_a5ee22e2-f9ed-4c2a-baf1-6939101fdc2a" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_a5ee22e2-f9ed-4c2a-baf1-6939101fdc2a_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_RepurchaseAgreementCounterpartyNameDomain_db383b7e-2dd1-47c3-b73d-8d941ac39081" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_RepurchaseAgreementCounterpartyNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_CounterpartyNameAxis_a5ee22e2-f9ed-4c2a-baf1-6939101fdc2a" xlink:to="loc_srt_RepurchaseAgreementCounterpartyNameDomain_db383b7e-2dd1-47c3-b73d-8d941ac39081" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MolecularAssembliesIncMember_dfb3f740-1a33-4312-824e-1bc7871b1049" xlink:href="cdxs-20231231.xsd#cdxs_MolecularAssembliesIncMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RepurchaseAgreementCounterpartyNameDomain_db383b7e-2dd1-47c3-b73d-8d941ac39081" xlink:to="loc_cdxs_MolecularAssembliesIncMember_dfb3f740-1a33-4312-824e-1bc7871b1049" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionAxis_c2c19564-06c4-4ddb-9476-1652da1dbee0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable_ae8ec08c-0a05-40d0-a759-1458192e795a" xlink:to="loc_us-gaap_RelatedPartyTransactionAxis_c2c19564-06c4-4ddb-9476-1652da1dbee0" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionDomain_c2c19564-06c4-4ddb-9476-1652da1dbee0_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RelatedPartyTransactionAxis_c2c19564-06c4-4ddb-9476-1652da1dbee0" xlink:to="loc_us-gaap_RelatedPartyTransactionDomain_c2c19564-06c4-4ddb-9476-1652da1dbee0_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RelatedPartyTransactionDomain_b9f6c030-c7db-48db-86ef-659a79add5a9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RelatedPartyTransactionDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RelatedPartyTransactionAxis_c2c19564-06c4-4ddb-9476-1652da1dbee0" xlink:to="loc_us-gaap_RelatedPartyTransactionDomain_b9f6c030-c7db-48db-86ef-659a79add5a9" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_MasterCollaborationResearchAgreementMember_fa504493-9ce6-466d-b2e9-cbb24bc67d04" xlink:href="cdxs-20231231.xsd#cdxs_MasterCollaborationResearchAgreementMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyTransactionDomain_b9f6c030-c7db-48db-86ef-659a79add5a9" xlink:to="loc_cdxs_MasterCollaborationResearchAgreementMember_fa504493-9ce6-466d-b2e9-cbb24bc67d04" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentOwnedBalanceShares_823f571b-5ff1-40ac-9e66-d2f61e9896dc" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_InvestmentOwnedBalanceShares"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyTransactionLineItems_cf49ab96-f622-4f66-a0bd-90bbb0a7f962" xlink:to="loc_us-gaap_InvestmentOwnedBalanceShares_823f571b-5ff1-40ac-9e66-d2f61e9896dc" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsToAcquireOtherInvestments_415006fa-4b15-4f6f-ac65-e90ee16885e0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PaymentsToAcquireOtherInvestments"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyTransactionLineItems_cf49ab96-f622-4f66-a0bd-90bbb0a7f962" xlink:to="loc_us-gaap_PaymentsToAcquireOtherInvestments_415006fa-4b15-4f6f-ac65-e90ee16885e0" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_NonmonetaryTransactionGrossOperatingRevenueRecognized_34229235-b5a9-44c6-bdf4-206d486218b4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_NonmonetaryTransactionGrossOperatingRevenueRecognized"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RelatedPartyTransactionLineItems_cf49ab96-f622-4f66-a0bd-90bbb0a7f962" xlink:to="loc_us-gaap_NonmonetaryTransactionGrossOperatingRevenueRecognized_34229235-b5a9-44c6-bdf4-206d486218b4" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationConcentrationRiskDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#SegmentGeographicalandOtherRevenueInformationConcentrationRiskDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationConcentrationRiskDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskLineItems_216dca7e-a348-43f2-98d8-b5faebea85fc" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTable_b27572e3-26d1-4a02-98a7-7bb0ae33ca58" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ConcentrationRiskLineItems_216dca7e-a348-43f2-98d8-b5faebea85fc" xlink:to="loc_us-gaap_ConcentrationRiskTable_b27572e3-26d1-4a02-98a7-7bb0ae33ca58" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_MajorCustomersAxis_9644b643-915b-416f-ab39-b97b41c601c1" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_MajorCustomersAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ConcentrationRiskTable_b27572e3-26d1-4a02-98a7-7bb0ae33ca58" xlink:to="loc_srt_MajorCustomersAxis_9644b643-915b-416f-ab39-b97b41c601c1" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_NameOfMajorCustomerDomain_9644b643-915b-416f-ab39-b97b41c601c1_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_NameOfMajorCustomerDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_MajorCustomersAxis_9644b643-915b-416f-ab39-b97b41c601c1" xlink:to="loc_srt_NameOfMajorCustomerDomain_9644b643-915b-416f-ab39-b97b41c601c1_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_NameOfMajorCustomerDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_MajorCustomersAxis_9644b643-915b-416f-ab39-b97b41c601c1" xlink:to="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerAMember_5bcef2be-6936-4a03-8875-6af629538f3f" xlink:href="cdxs-20231231.xsd#cdxs_CustomerAMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:to="loc_cdxs_CustomerAMember_5bcef2be-6936-4a03-8875-6af629538f3f" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerBMember_4f5b19c5-2752-4e34-ad8e-ad168755d438" xlink:href="cdxs-20231231.xsd#cdxs_CustomerBMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:to="loc_cdxs_CustomerBMember_4f5b19c5-2752-4e34-ad8e-ad168755d438" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerCMember_1ef40575-d533-41b7-b9ab-5cf07b0b782b" xlink:href="cdxs-20231231.xsd#cdxs_CustomerCMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:to="loc_cdxs_CustomerCMember_1ef40575-d533-41b7-b9ab-5cf07b0b782b" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerDMember_2413bfab-ae73-4787-b6fe-f4c2bf2778d9" xlink:href="cdxs-20231231.xsd#cdxs_CustomerDMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:to="loc_cdxs_CustomerDMember_2413bfab-ae73-4787-b6fe-f4c2bf2778d9" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerEMember_0a23f481-3d31-40d8-bd6b-73fdfe29d7ee" xlink:href="cdxs-20231231.xsd#cdxs_CustomerEMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:to="loc_cdxs_CustomerEMember_0a23f481-3d31-40d8-bd6b-73fdfe29d7ee" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerFMember_db1ff85b-eddc-4b46-82c8-7e63abc20553" xlink:href="cdxs-20231231.xsd#cdxs_CustomerFMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_cdb3a080-8efa-45c2-81e3-4eae20bf7ec5" xlink:to="loc_cdxs_CustomerFMember_db1ff85b-eddc-4b46-82c8-7e63abc20553" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_6bea4aae-4924-43ca-aafd-897ecbda1864" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ConcentrationRiskTable_b27572e3-26d1-4a02-98a7-7bb0ae33ca58" xlink:to="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_6bea4aae-4924-43ca-aafd-897ecbda1864" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_6bea4aae-4924-43ca-aafd-897ecbda1864_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_6bea4aae-4924-43ca-aafd-897ecbda1864" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_6bea4aae-4924-43ca-aafd-897ecbda1864_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_c639cfb1-36bf-49ca-ba13-0518bc45af3a" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_6bea4aae-4924-43ca-aafd-897ecbda1864" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_c639cfb1-36bf-49ca-ba13-0518bc45af3a" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SalesRevenueProductLineMember_eb5519be-544d-4d36-a8e4-212b0283f432" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SalesRevenueProductLineMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_c639cfb1-36bf-49ca-ba13-0518bc45af3a" xlink:to="loc_us-gaap_SalesRevenueProductLineMember_eb5519be-544d-4d36-a8e4-212b0283f432" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsReceivableMember_147738a3-510b-4912-80c1-4703fcaa2f6e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AccountsReceivableMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_c639cfb1-36bf-49ca-ba13-0518bc45af3a" xlink:to="loc_us-gaap_AccountsReceivableMember_147738a3-510b-4912-80c1-4703fcaa2f6e" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByTypeAxis_87054786-6a5d-4336-ad46-58fe22890d74" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ConcentrationRiskTable_b27572e3-26d1-4a02-98a7-7bb0ae33ca58" xlink:to="loc_us-gaap_ConcentrationRiskByTypeAxis_87054786-6a5d-4336-ad46-58fe22890d74" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_87054786-6a5d-4336-ad46-58fe22890d74_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_87054786-6a5d-4336-ad46-58fe22890d74" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_87054786-6a5d-4336-ad46-58fe22890d74_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_23edff4f-5f9b-4c79-9d64-c4d68807c3a2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_87054786-6a5d-4336-ad46-58fe22890d74" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_23edff4f-5f9b-4c79-9d64-c4d68807c3a2" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CustomerConcentrationRiskMember_58dc3f66-b54c-419e-96dd-b7672db53f7b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CustomerConcentrationRiskMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskTypeDomain_23edff4f-5f9b-4c79-9d64-c4d68807c3a2" xlink:to="loc_us-gaap_CustomerConcentrationRiskMember_58dc3f66-b54c-419e-96dd-b7672db53f7b" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskPercentage1_a8fc979d-80de-4988-95cf-bf99112e31d0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ConcentrationRiskPercentage1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskLineItems_216dca7e-a348-43f2-98d8-b5faebea85fc" xlink:to="loc_us-gaap_ConcentrationRiskPercentage1_a8fc979d-80de-4988-95cf-bf99112e31d0" xlink:type="arc" order="0"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationRevenuesDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#SegmentGeographicalandOtherRevenueInformationRevenuesDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationRevenuesDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenuesFromExternalCustomersAndLongLivedAssetsLineItems_9828fa5b-4dfa-4668-8eb0-54c860ab9713" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenuesFromExternalCustomersAndLongLivedAssetsLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable_22517090-30fc-482e-bff7-f7981ec54eb9" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_RevenuesFromExternalCustomersAndLongLivedAssetsLineItems_9828fa5b-4dfa-4668-8eb0-54c860ab9713" xlink:to="loc_us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable_22517090-30fc-482e-bff7-f7981ec54eb9" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_StatementGeographicalAxis_1257e1fd-fe4e-4546-8bc9-d61151220a4d" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_StatementGeographicalAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable_22517090-30fc-482e-bff7-f7981ec54eb9" xlink:to="loc_srt_StatementGeographicalAxis_1257e1fd-fe4e-4546-8bc9-d61151220a4d" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_1257e1fd-fe4e-4546-8bc9-d61151220a4d_default" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_SegmentGeographicalDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_StatementGeographicalAxis_1257e1fd-fe4e-4546-8bc9-d61151220a4d" xlink:to="loc_srt_SegmentGeographicalDomain_1257e1fd-fe4e-4546-8bc9-d61151220a4d_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_SegmentGeographicalDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_StatementGeographicalAxis_1257e1fd-fe4e-4546-8bc9-d61151220a4d" xlink:to="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_AmericasMember_dd2bdc10-663f-489b-8709-e56908c2c768" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_AmericasMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:to="loc_srt_AmericasMember_dd2bdc10-663f-489b-8709-e56908c2c768" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EMEAMember_4e3e2020-2934-41c6-99ae-9513e291c463" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EMEAMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:to="loc_us-gaap_EMEAMember_4e3e2020-2934-41c6-99ae-9513e291c463" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_srt_AsiaPacificMember_92255e48-8021-4fd6-a6c0-229d6ffe1c2c" xlink:href="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd#srt_AsiaPacificMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:to="loc_srt_AsiaPacificMember_92255e48-8021-4fd6-a6c0-229d6ffe1c2c" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_country_US_a26022b7-6973-46a6-ba4f-c5a90acbbdfb" xlink:href="https://xbrl.sec.gov/country/2023/country-2023.xsd#country_US"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:to="loc_country_US_a26022b7-6973-46a6-ba4f-c5a90acbbdfb" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_country_IE_3c64d475-0c60-4277-a3e3-8d13f5d2f92b" xlink:href="https://xbrl.sec.gov/country/2023/country-2023.xsd#country_IE"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:to="loc_country_IE_3c64d475-0c60-4277-a3e3-8d13f5d2f92b" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_country_CH_6b8bfae8-c13d-46ff-9ee1-4f082ca5c625" xlink:href="https://xbrl.sec.gov/country/2023/country-2023.xsd#country_CH"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:to="loc_country_CH_6b8bfae8-c13d-46ff-9ee1-4f082ca5c625" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_country_CN_c501fc75-aca4-4352-ac90-a90e9297a5ca" xlink:href="https://xbrl.sec.gov/country/2023/country-2023.xsd#country_CN"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_0ed44e9c-0b64-44c5-bd23-5b423d4895ce" xlink:to="loc_country_CN_c501fc75-aca4-4352-ac90-a90e9297a5ca" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenuesAbstract_860ff627-eb51-4c76-a8f9-e4fff05c2639" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenuesAbstract"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RevenuesFromExternalCustomersAndLongLivedAssetsLineItems_9828fa5b-4dfa-4668-8eb0-54c860ab9713" xlink:to="loc_us-gaap_RevenuesAbstract_860ff627-eb51-4c76-a8f9-e4fff05c2639" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_110c1689-c927-4f17-a1d9-5d9f606c76cd" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RevenuesAbstract_860ff627-eb51-4c76-a8f9-e4fff05c2639" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_110c1689-c927-4f17-a1d9-5d9f606c76cd" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_NoncurrentAssets_1d2c5685-37e8-4008-bf08-44475493e0b4" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_NoncurrentAssets"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RevenuesAbstract_860ff627-eb51-4c76-a8f9-e4fff05c2639" xlink:to="loc_us-gaap_NoncurrentAssets_1d2c5685-37e8-4008-bf08-44475493e0b4" xlink:type="arc" order="2"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/AllowanceforCreditLossesSummaryofAccountsReceivablebyAgingCategoryDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#AllowanceforCreditLossesSummaryofAccountsReceivablebyAgingCategoryDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/AllowanceforCreditLossesSummaryofAccountsReceivablebyAgingCategoryDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancingReceivableAllowanceForCreditLossesLineItems_bee2584f-b092-4331-972e-842c1a588f59" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancingReceivableAllowanceForCreditLossesLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfFinancingReceivableAllowanceForCreditLossesTable_26300373-d9d1-4f1d-a777-3b49653d8179" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfFinancingReceivableAllowanceForCreditLossesTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_FinancingReceivableAllowanceForCreditLossesLineItems_bee2584f-b092-4331-972e-842c1a588f59" xlink:to="loc_us-gaap_ScheduleOfFinancingReceivableAllowanceForCreditLossesTable_26300373-d9d1-4f1d-a777-3b49653d8179" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancingReceivablesPeriodPastDueAxis_05cbcff7-0312-4d49-9482-5525b1cb2030" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancingReceivablesPeriodPastDueAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfFinancingReceivableAllowanceForCreditLossesTable_26300373-d9d1-4f1d-a777-3b49653d8179" xlink:to="loc_us-gaap_FinancingReceivablesPeriodPastDueAxis_05cbcff7-0312-4d49-9482-5525b1cb2030" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_05cbcff7-0312-4d49-9482-5525b1cb2030_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancingReceivablesPeriodPastDueDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_FinancingReceivablesPeriodPastDueAxis_05cbcff7-0312-4d49-9482-5525b1cb2030" xlink:to="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_05cbcff7-0312-4d49-9482-5525b1cb2030_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_0b34f688-3481-4850-abbd-41ca7c464811" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancingReceivablesPeriodPastDueDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_FinancingReceivablesPeriodPastDueAxis_05cbcff7-0312-4d49-9482-5525b1cb2030" xlink:to="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_0b34f688-3481-4850-abbd-41ca7c464811" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancialAssetNotPastDueMember_572faddb-d064-4506-b560-628d257fbf29" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancialAssetNotPastDueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_0b34f688-3481-4850-abbd-41ca7c464811" xlink:to="loc_us-gaap_FinancialAssetNotPastDueMember_572faddb-d064-4506-b560-628d257fbf29" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancingReceivables30To59DaysPastDueMember_c095b6eb-96d0-46b6-8b53-cea4505ec9c6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancingReceivables30To59DaysPastDueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_0b34f688-3481-4850-abbd-41ca7c464811" xlink:to="loc_us-gaap_FinancingReceivables30To59DaysPastDueMember_c095b6eb-96d0-46b6-8b53-cea4505ec9c6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancingReceivables60To89DaysPastDueMember_108e1920-06a4-4f00-ac51-1570c05c6fec" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancingReceivables60To89DaysPastDueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_0b34f688-3481-4850-abbd-41ca7c464811" xlink:to="loc_us-gaap_FinancingReceivables60To89DaysPastDueMember_108e1920-06a4-4f00-ac51-1570c05c6fec" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancingReceivablesEqualToGreaterThan90DaysPastDueMember_c2b081ed-ce04-4c57-ae61-97ef69aa1c5e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_FinancingReceivablesEqualToGreaterThan90DaysPastDueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_0b34f688-3481-4850-abbd-41ca7c464811" xlink:to="loc_us-gaap_FinancingReceivablesEqualToGreaterThan90DaysPastDueMember_c2b081ed-ce04-4c57-ae61-97ef69aa1c5e" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_FinancialReceivablesPastDueMember_e992d247-78e6-4de8-9e09-668d7c70668f" xlink:href="cdxs-20231231.xsd#cdxs_FinancialReceivablesPastDueMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FinancingReceivablesPeriodPastDueDomain_0b34f688-3481-4850-abbd-41ca7c464811" xlink:to="loc_cdxs_FinancialReceivablesPastDueMember_e992d247-78e6-4de8-9e09-668d7c70668f" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsReceivableGross_3092f67d-f197-4983-9950-88891b15d7b6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_AccountsReceivableGross"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FinancingReceivableAllowanceForCreditLossesLineItems_bee2584f-b092-4331-972e-842c1a588f59" xlink:to="loc_us-gaap_AccountsReceivableGross_3092f67d-f197-4983-9950-88891b15d7b6" xlink:type="arc" order="0"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/RestructuringChargesDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#RestructuringChargesDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/RestructuringChargesDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestructuringCostAndReserveLineItems_4af0884e-eb7c-4299-a50b-34bf8107d814" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestructuringCostAndReserveLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfRestructuringAndRelatedCostsTable_16ebf407-6929-4390-85f4-d8e9664b62e6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ScheduleOfRestructuringAndRelatedCostsTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_RestructuringCostAndReserveLineItems_4af0884e-eb7c-4299-a50b-34bf8107d814" xlink:to="loc_us-gaap_ScheduleOfRestructuringAndRelatedCostsTable_16ebf407-6929-4390-85f4-d8e9664b62e6" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestructuringCostAndReserveAxis_39594791-3e17-48e2-b07a-af6368406ee6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestructuringCostAndReserveAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfRestructuringAndRelatedCostsTable_16ebf407-6929-4390-85f4-d8e9664b62e6" xlink:to="loc_us-gaap_RestructuringCostAndReserveAxis_39594791-3e17-48e2-b07a-af6368406ee6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfRestructuringDomain_39594791-3e17-48e2-b07a-af6368406ee6_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfRestructuringDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_RestructuringCostAndReserveAxis_39594791-3e17-48e2-b07a-af6368406ee6" xlink:to="loc_us-gaap_TypeOfRestructuringDomain_39594791-3e17-48e2-b07a-af6368406ee6_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_TypeOfRestructuringDomain_38941bdc-3c3a-4144-9fe3-7854c7e66bb6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_TypeOfRestructuringDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_RestructuringCostAndReserveAxis_39594791-3e17-48e2-b07a-af6368406ee6" xlink:to="loc_us-gaap_TypeOfRestructuringDomain_38941bdc-3c3a-4144-9fe3-7854c7e66bb6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_OneTimeTerminationBenefitsMember_5c05cb1f-4a92-464e-ad05-2d4943efb0e6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_OneTimeTerminationBenefitsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TypeOfRestructuringDomain_38941bdc-3c3a-4144-9fe3-7854c7e66bb6" xlink:to="loc_us-gaap_OneTimeTerminationBenefitsMember_5c05cb1f-4a92-464e-ad05-2d4943efb0e6" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeSeveranceMember_ea78e09e-83cb-4312-ac1b-496271349386" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeSeveranceMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TypeOfRestructuringDomain_38941bdc-3c3a-4144-9fe3-7854c7e66bb6" xlink:to="loc_us-gaap_EmployeeSeveranceMember_ea78e09e-83cb-4312-ac1b-496271349386" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestructuringAndRelatedCostNumberOfPositionsEliminatedPeriodPercent_59f61e14-43eb-4f88-befd-99ba78fd81a0" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestructuringAndRelatedCostNumberOfPositionsEliminatedPeriodPercent"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestructuringCostAndReserveLineItems_4af0884e-eb7c-4299-a50b-34bf8107d814" xlink:to="loc_us-gaap_RestructuringAndRelatedCostNumberOfPositionsEliminatedPeriodPercent_59f61e14-43eb-4f88-befd-99ba78fd81a0" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestructuringCharges_29b8b670-1a42-4119-96f4-06d5b88c39f1" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestructuringCharges"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RestructuringCostAndReserveLineItems_4af0884e-eb7c-4299-a50b-34bf8107d814" xlink:to="loc_us-gaap_RestructuringCharges_29b8b670-1a42-4119-96f4-06d5b88c39f1" xlink:type="arc" order="1"/>
</link:definitionLink>
<link:roleRef roleURI="http://www.codexis.com/role/SubsequentEventsDetails" xlink:type="simple" xlink:href="cdxs-20231231.xsd#SubsequentEventsDetails"/>
<link:definitionLink xlink:role="http://www.codexis.com/role/SubsequentEventsDetails" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventLineItems"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTable_189039fd-28f9-4e6b-9627-d133e2a6a5b5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTable"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_us-gaap_SubsequentEventTable_189039fd-28f9-4e6b-9627-d133e2a6a5b5" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentAxis_95cb3d6d-8f62-4bf3-b052-bf56097b26c8" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtInstrumentAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_SubsequentEventTable_189039fd-28f9-4e6b-9627-d133e2a6a5b5" xlink:to="loc_us-gaap_DebtInstrumentAxis_95cb3d6d-8f62-4bf3-b052-bf56097b26c8" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentNameDomain_95cb3d6d-8f62-4bf3-b052-bf56097b26c8_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtInstrumentNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_DebtInstrumentAxis_95cb3d6d-8f62-4bf3-b052-bf56097b26c8" xlink:to="loc_us-gaap_DebtInstrumentNameDomain_95cb3d6d-8f62-4bf3-b052-bf56097b26c8_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentNameDomain_76c04a0b-485a-41a9-95ba-047b3ce8709f" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtInstrumentNameDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_DebtInstrumentAxis_95cb3d6d-8f62-4bf3-b052-bf56097b26c8" xlink:to="loc_us-gaap_DebtInstrumentNameDomain_76c04a0b-485a-41a9-95ba-047b3ce8709f" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TermLoansMember_0b3b12e5-c73c-4b41-8b06-5ff4773fb338" xlink:href="cdxs-20231231.xsd#cdxs_TermLoansMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_76c04a0b-485a-41a9-95ba-047b3ce8709f" xlink:to="loc_cdxs_TermLoansMember_0b3b12e5-c73c-4b41-8b06-5ff4773fb338" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TermLoansFirstTrancheMember_0ced14ee-1d02-47c1-91f7-fa40cdae65e1" xlink:href="cdxs-20231231.xsd#cdxs_TermLoansFirstTrancheMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_76c04a0b-485a-41a9-95ba-047b3ce8709f" xlink:to="loc_cdxs_TermLoansFirstTrancheMember_0ced14ee-1d02-47c1-91f7-fa40cdae65e1" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TermLoansSecondTrancheMember_92362483-d82e-4ffc-bb6f-885aefea5b96" xlink:href="cdxs-20231231.xsd#cdxs_TermLoansSecondTrancheMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_76c04a0b-485a-41a9-95ba-047b3ce8709f" xlink:to="loc_cdxs_TermLoansSecondTrancheMember_92362483-d82e-4ffc-bb6f-885aefea5b96" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_TermLoanMember_152c4896-88f3-4141-a689-012b52665d34" xlink:href="cdxs-20231231.xsd#cdxs_TermLoanMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_76c04a0b-485a-41a9-95ba-047b3ce8709f" xlink:to="loc_cdxs_TermLoanMember_152c4896-88f3-4141-a689-012b52665d34" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeAxis_18f7483e-8bbd-4f6d-8bc8-d2d4c8c5003d" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_SubsequentEventTable_189039fd-28f9-4e6b-9627-d133e2a6a5b5" xlink:to="loc_us-gaap_SubsequentEventTypeAxis_18f7483e-8bbd-4f6d-8bc8-d2d4c8c5003d" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_18f7483e-8bbd-4f6d-8bc8-d2d4c8c5003d_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_18f7483e-8bbd-4f6d-8bc8-d2d4c8c5003d" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_18f7483e-8bbd-4f6d-8bc8-d2d4c8c5003d_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_e406178b-e285-4773-b820-843e85edc8c6" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventTypeDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_18f7483e-8bbd-4f6d-8bc8-d2d4c8c5003d" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_e406178b-e285-4773-b820-843e85edc8c6" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventMember_6db9debe-3ed0-4b01-8d8a-8d64b4018f14" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_SubsequentEventMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventTypeDomain_e406178b-e285-4773-b820-843e85edc8c6" xlink:to="loc_us-gaap_SubsequentEventMember_6db9debe-3ed0-4b01-8d8a-8d64b4018f14" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_VariableRateAxis_d21f0e29-5db4-40ce-8f01-14f3be43f449" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_VariableRateAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_SubsequentEventTable_189039fd-28f9-4e6b-9627-d133e2a6a5b5" xlink:to="loc_us-gaap_VariableRateAxis_d21f0e29-5db4-40ce-8f01-14f3be43f449" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_VariableRateDomain_d21f0e29-5db4-40ce-8f01-14f3be43f449_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_VariableRateDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_VariableRateAxis_d21f0e29-5db4-40ce-8f01-14f3be43f449" xlink:to="loc_us-gaap_VariableRateDomain_d21f0e29-5db4-40ce-8f01-14f3be43f449_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_VariableRateDomain_f1541799-c01e-43f3-80e6-12b57f2f1089" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_VariableRateDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_VariableRateAxis_d21f0e29-5db4-40ce-8f01-14f3be43f449" xlink:to="loc_us-gaap_VariableRateDomain_f1541799-c01e-43f3-80e6-12b57f2f1089" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PrimeRateMember_cfa94199-59b7-4d58-9d60-70c3af825ff5" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PrimeRateMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_VariableRateDomain_f1541799-c01e-43f3-80e6-12b57f2f1089" xlink:to="loc_us-gaap_PrimeRateMember_cfa94199-59b7-4d58-9d60-70c3af825ff5" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementClassOfStockAxis_cea51f28-4c1f-424f-a828-c7e723cb868c" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_StatementClassOfStockAxis"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_SubsequentEventTable_189039fd-28f9-4e6b-9627-d133e2a6a5b5" xlink:to="loc_us-gaap_StatementClassOfStockAxis_cea51f28-4c1f-424f-a828-c7e723cb868c" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_cea51f28-4c1f-424f-a828-c7e723cb868c_default" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementClassOfStockAxis_cea51f28-4c1f-424f-a828-c7e723cb868c" xlink:to="loc_us-gaap_ClassOfStockDomain_cea51f28-4c1f-424f-a828-c7e723cb868c_default" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockDomain_481697aa-c756-4094-9ad2-989c690536d2" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfStockDomain"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementClassOfStockAxis_cea51f28-4c1f-424f-a828-c7e723cb868c" xlink:to="loc_us-gaap_ClassOfStockDomain_481697aa-c756-4094-9ad2-989c690536d2" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockMember_f84e6d06-32cd-4b2b-b2af-d4bf85d9c1ee" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_CommonStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockDomain_481697aa-c756-4094-9ad2-989c690536d2" xlink:to="loc_us-gaap_CommonStockMember_f84e6d06-32cd-4b2b-b2af-d4bf85d9c1ee" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentTerm_267d52df-8324-4d4a-8890-6c538cdfdbeb" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtInstrumentTerm"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_us-gaap_DebtInstrumentTerm_267d52df-8324-4d4a-8890-6c538cdfdbeb" xlink:type="arc" order="0"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentFaceAmount_8f67ca14-52b0-40ab-a354-b8260f94815b" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtInstrumentFaceAmount"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_us-gaap_DebtInstrumentFaceAmount_8f67ca14-52b0-40ab-a354-b8260f94815b" xlink:type="arc" order="1"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_DebtInstrumentNumberOfTranches_f45cbcf2-ed71-4ed3-ad6b-56318bca9dfd" xlink:href="cdxs-20231231.xsd#cdxs_DebtInstrumentNumberOfTranches"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_cdxs_DebtInstrumentNumberOfTranches_f45cbcf2-ed71-4ed3-ad6b-56318bca9dfd" xlink:type="arc" order="2"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_DebtInstrumentInterestPeriod_2b3c18bb-e812-4401-9cd3-ec94fef5a8eb" xlink:href="cdxs-20231231.xsd#cdxs_DebtInstrumentInterestPeriod"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_cdxs_DebtInstrumentInterestPeriod_2b3c18bb-e812-4401-9cd3-ec94fef5a8eb" xlink:type="arc" order="3"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentInterestRateStatedPercentage_21ee4e94-76b3-48e5-b1d1-0e0374dd6a06" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_us-gaap_DebtInstrumentInterestRateStatedPercentage_21ee4e94-76b3-48e5-b1d1-0e0374dd6a06" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentBasisSpreadOnVariableRate1_a71d9db6-f458-4a67-97a2-c3482f7f3711" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_DebtInstrumentBasisSpreadOnVariableRate1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_us-gaap_DebtInstrumentBasisSpreadOnVariableRate1_a71d9db6-f458-4a67-97a2-c3482f7f3711" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_096e47c4-fb2a-45ab-bdaa-8775df306b39" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_096e47c4-fb2a-45ab-bdaa-8775df306b39" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1_b82cedda-e11c-45dd-b5c7-810670b6a84e" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_106bb8e3-87dd-42a4-87e5-b28dbb609c20" xlink:to="loc_us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1_b82cedda-e11c-45dd-b5c7-810670b6a84e" xlink:type="arc" order="7"/>
</link:definitionLink>
<link:roleRef roleURI="http://xbrl.sec.gov/ecd/AwardTypeOnly" xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2023/ecd-2023.xsd#AwardTypeOnly"/>
<link:definitionLink xlink:role="http://xbrl.sec.gov/ecd/AwardTypeOnly" xlink:type="extended">
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_EmployeeStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_us-gaap_EmployeeStockMember" xlink:type="arc" order="4"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_IncentiveStockOptionsMember_e3d3c083-131b-4535-b15e-0adaf9823141" xlink:href="cdxs-20231231.xsd#cdxs_IncentiveStockOptionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_cdxs_IncentiveStockOptionsMember_e3d3c083-131b-4535-b15e-0adaf9823141" xlink:type="arc" order="5"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_NonStatutoryStockOptionsMember_587f2951-d330-4a37-8771-624e450ad9df" xlink:href="cdxs-20231231.xsd#cdxs_NonStatutoryStockOptionsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_cdxs_NonStatutoryStockOptionsMember_587f2951-d330-4a37-8771-624e450ad9df" xlink:type="arc" order="6"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedStockUnitsRSUMember" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedStockUnitsRSUMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_us-gaap_RestrictedStockUnitsRSUMember" xlink:type="arc" order="7"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_PerformanceSharesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_PerformanceSharesMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_us-gaap_PerformanceSharesMember" xlink:type="arc" order="8"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceShareUnitsPSUsMember_5c60d2e4-e9e9-4794-8d0b-ae696437a6d6" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceShareUnitsPSUsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_cdxs_PerformanceShareUnitsPSUsMember_5c60d2e4-e9e9-4794-8d0b-ae696437a6d6" xlink:type="arc" order="9"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceBasedOptionsPBOsMember_e5e81679-6229-4855-ac33-35ecf33d0687" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceBasedOptionsPBOsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_cdxs_PerformanceBasedOptionsPBOsMember_e5e81679-6229-4855-ac33-35ecf33d0687" xlink:type="arc" order="10"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_RSUsAndRSAsMember_378cb23d-1b56-4d30-be98-f787439a6d8d" xlink:href="cdxs-20231231.xsd#cdxs_RSUsAndRSAsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_cdxs_RSUsAndRSAsMember_378cb23d-1b56-4d30-be98-f787439a6d8d" xlink:type="arc" order="11"/>
<link:loc xlink:type="locator" xlink:label="loc_cdxs_PerformanceStockUnitsMember_20473a88-1ff2-4107-adc6-5a3c4e77394b" xlink:href="cdxs-20231231.xsd#cdxs_PerformanceStockUnitsMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_cdxs_PerformanceStockUnitsMember_20473a88-1ff2-4107-adc6-5a3c4e77394b" xlink:type="arc" order="12"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_ShareBasedPaymentArrangementNonemployeeMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_us-gaap_ShareBasedPaymentArrangementNonemployeeMember" xlink:type="arc" order="13"/>
<link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedStockMember" xlink:href="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd#us-gaap_RestrictedStockMember"/>
<link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="loc_us-gaap_RestrictedStockMember" xlink:type="arc" order="14"/>
</link:definitionLink>
</link:linkbase>


2 Subsequent Filings that Reference this Filing

  As Of               Filer                 Filing    For·On·As Docs:Size             Issuer                      Filing Agent

 5/02/24  Codexis, Inc.                     10-Q        3/31/24   76:5.8M
 5/02/24  Codexis, Inc.                     S-3                    6:1M                                     Donnelley … Solutions/FA


25 Previous Filings that this Filing References

  As Of               Filer                 Filing    For·On·As Docs:Size             Issuer                      Filing Agent

 2/13/24  Codexis, Inc.                     8-K:1,2,3,9 2/13/24   11:208K                                   Donnelley … Solutions/FA
 2/09/24  Codexis, Inc.                     8-K:5,9     2/08/24   11:360K                                   Donnelley … Solutions/FA
11/03/23  Codexis, Inc.                     10-Q        9/30/23   92:8.8M
 8/03/23  Codexis, Inc.                     10-Q        6/30/23   92:8.4M
 6/16/23  Codexis, Inc.                     8-K:5,9     6/13/23   13:287K                                   Donnelley … Solutions/FA
 2/27/23  Codexis, Inc.                     10-K       12/31/22  121:15M
 1/09/23  Codexis, Inc.                     S-8         1/09/23    7:328K                                   Donnelley … Solutions/FA
11/04/22  Codexis, Inc.                     10-Q        9/30/22   86:9.5M
 5/07/21  Codexis, Inc.                     10-Q        3/31/21   85:7.7M
 5/07/21  Codexis, Inc.                     8-K:1,9     5/07/21   12:398K                                   Donnelley … Solutions/FA
11/06/19  Codexis, Inc.                     10-Q        9/30/19   82:10M
 6/21/19  Codexis, Inc.                     S-8         6/21/19    9:454K                                   Donnelley … Solutions/FA
 5/08/19  Codexis, Inc.                     10-Q        3/31/19   80:7.6M
 3/15/18  Codexis, Inc.                     10-K       12/31/17   89:10M
11/08/16  Codexis, Inc.                     10-Q        9/30/16   65:5.7M
 8/09/16  Codexis, Inc.                     10-Q        6/30/16   62:5.3M
11/07/12  Codexis, Inc.                     10-Q        9/30/12   68:5.1M                                   Donnelley … Solutions/FA
 9/04/12  Codexis, Inc.                     8-K:1,2,3,5 8/28/12    5:380K                                   Donnelley … Solutions/FA
 8/09/12  Codexis, Inc.                     10-Q        6/30/12    9:1.1M                                   Donnelley … Solutions/FA
 5/06/11  Codexis, Inc.                     10-Q        3/31/11    5:927K                                   Donnelley … Solutions/FA
11/04/10  Codexis, Inc.                     10-Q        9/30/10    5:820K                                   Donnelley … Solutions/FA
10/28/10  Codexis, Inc.                     8-K:1,2,9  10/28/10    4:463K                                   Donnelley … Solutions/FA
 5/28/10  Codexis, Inc.                     10-Q        3/31/10    6:850K                                   Donnelley … Solutions/FA
 3/31/10  Codexis, Inc.                     S-1/A                  9:3.7M                                   Donnelley … Solutions/FA
12/28/09  Codexis, Inc.                     S-1                   37:5.9M                                   Donnelley … Solutions/FA
Top
Filing Submission 0001200375-24-000009   –   Alternative Formats (Word / Rich Text, HTML, Plain Text, et al.)

Copyright © 2024 Fran Finnegan & Company LLC – All Rights Reserved.
AboutPrivacyRedactionsHelp — Sat., May 11, 9:38:52.4am ET