<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with Wdesk from Workiva-->
<!--Copyright 2021 Workiva-->
<!--r:541c6ab8-8ba6-4ba8-bfdd-0df8c84312b6,g:3f3c32f1-4477-43fb-a57c-d3c85e0ff788-->
<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" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.codexis.com/role/Cover" xlink:type="simple" xlink:href="cdxs-20211014.xsd#Cover"/>
  <link:presentationLink xlink:role="http://www.codexis.com/role/Cover" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_CoverAbstract"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityCentralIndexKey_372ae07b-5cb5-4dbc-95a7-daf4554c2d30" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityCentralIndexKey"/>
    <link:presentationArc order="1" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityCentralIndexKey_372ae07b-5cb5-4dbc-95a7-daf4554c2d30" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentType_6d745e73-950d-48ed-aed8-265a90200f33" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentType"/>
    <link:presentationArc order="2" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_DocumentType_6d745e73-950d-48ed-aed8-265a90200f33" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentPeriodEndDate_56f98522-d855-4232-808a-6d7c36e82e54" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentPeriodEndDate"/>
    <link:presentationArc order="3" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_DocumentPeriodEndDate_56f98522-d855-4232-808a-6d7c36e82e54" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityRegistrantName_811bacf4-9fda-49a3-8e19-796db0e9a6b1" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityRegistrantName"/>
    <link:presentationArc order="4" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityRegistrantName_811bacf4-9fda-49a3-8e19-796db0e9a6b1" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityIncorporationStateCountryCode_29a41392-67d5-4498-a80b-6058dba7123e" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityIncorporationStateCountryCode"/>
    <link:presentationArc order="5" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityIncorporationStateCountryCode_29a41392-67d5-4498-a80b-6058dba7123e" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityFileNumber_e645c5b6-4073-4f35-a80a-02814c7ca3c4" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityFileNumber"/>
    <link:presentationArc order="6" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityFileNumber_e645c5b6-4073-4f35-a80a-02814c7ca3c4" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityTaxIdentificationNumber_d0c057e5-7a7c-4978-a8b5-943073c3f780" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityTaxIdentificationNumber"/>
    <link:presentationArc order="7" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityTaxIdentificationNumber_d0c057e5-7a7c-4978-a8b5-943073c3f780" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressCityOrTown_98741925-a255-401c-aa3f-80fc7a7b9574" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressCityOrTown"/>
    <link:presentationArc order="8" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityAddressCityOrTown_98741925-a255-401c-aa3f-80fc7a7b9574" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressPostalZipCode_64da3ec5-f1ce-43e2-854b-8de2448afb1c" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressPostalZipCode"/>
    <link:presentationArc order="9" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityAddressPostalZipCode_64da3ec5-f1ce-43e2-854b-8de2448afb1c" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_CityAreaCode_cead250d-863b-4832-94ec-437b0c60f96a" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_CityAreaCode"/>
    <link:presentationArc order="10" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_CityAreaCode_cead250d-863b-4832-94ec-437b0c60f96a" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_LocalPhoneNumber_76c86f24-2245-478b-9cb3-cdeff9544e86" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_LocalPhoneNumber"/>
    <link:presentationArc order="11" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_LocalPhoneNumber_76c86f24-2245-478b-9cb3-cdeff9544e86" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_WrittenCommunications_c3d3bf34-c5b0-41d8-80f4-7f7a5aed5f46" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_WrittenCommunications"/>
    <link:presentationArc order="12" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_WrittenCommunications_c3d3bf34-c5b0-41d8-80f4-7f7a5aed5f46" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SolicitingMaterial_4011a69e-2482-4a0c-8aed-c852f0f38227" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_SolicitingMaterial"/>
    <link:presentationArc order="13" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_SolicitingMaterial_4011a69e-2482-4a0c-8aed-c852f0f38227" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementTenderOffer_68cc85bf-5189-4ca9-8a64-b9ac438cf9f7" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_PreCommencementTenderOffer"/>
    <link:presentationArc order="14" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_PreCommencementTenderOffer_68cc85bf-5189-4ca9-8a64-b9ac438cf9f7" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementIssuerTenderOffer_d6fabeaa-0e70-41ad-9d7a-f9ef746f4066" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_PreCommencementIssuerTenderOffer"/>
    <link:presentationArc order="15" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_PreCommencementIssuerTenderOffer_d6fabeaa-0e70-41ad-9d7a-f9ef746f4066" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_Security12bTitle_6af46676-297a-42cf-97c1-776bfd3d4843" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_Security12bTitle"/>
    <link:presentationArc order="16" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_Security12bTitle_6af46676-297a-42cf-97c1-776bfd3d4843" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_TradingSymbol_597a8b13-0804-4d04-8d7e-3c65b3d9cacd" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_TradingSymbol"/>
    <link:presentationArc order="17" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_TradingSymbol_597a8b13-0804-4d04-8d7e-3c65b3d9cacd" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SecurityExchangeName_18d87ee2-7064-4417-af59-46bdc03fae62" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_SecurityExchangeName"/>
    <link:presentationArc order="18" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_SecurityExchangeName_18d87ee2-7064-4417-af59-46bdc03fae62" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityEmergingGrowthCompany_7c122f29-2eb4-4ce8-bc33-fa490d87d223" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityEmergingGrowthCompany"/>
    <link:presentationArc order="19" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityEmergingGrowthCompany_7c122f29-2eb4-4ce8-bc33-fa490d87d223" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_AmendmentFlag_d55027d5-fe71-49e8-94db-8c4ea2a693fe" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_AmendmentFlag"/>
    <link:presentationArc order="20" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_AmendmentFlag_d55027d5-fe71-49e8-94db-8c4ea2a693fe" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressAddressLine1_051aae6c-c5e8-4e51-851f-c5acd88ba98c" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressAddressLine1"/>
    <link:presentationArc order="21" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityAddressAddressLine1_051aae6c-c5e8-4e51-851f-c5acd88ba98c" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressStateOrProvince_5ea524df-4b29-4226-a6a3-1fe0cd0e16be" xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressStateOrProvince"/>
    <link:presentationArc order="22" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_0966a7b2-e891-40b1-89b1-a6be1683fbf5" xlink:to="loc_dei_EntityAddressStateOrProvince_5ea524df-4b29-4226-a6a3-1fe0cd0e16be" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
</link:linkbase>
