Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reportingcompany, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company”and “emerging growth company” in Rule12b-2 of the Exchange Act. Emerging growth companyIf an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for Indicate by check mark whether the registrant is a shell company (as defined in Rule12b-2 of the Exchange Act).Yes☐No☒Asof May9, 2025, there were82,844,849shares of the registrant’s Common Stock, par value $0.0001 per share, outstanding. Codexis, Inc.Quarterly Report on Form 10-Q TABLE OF CONTENTS Defaults Upon Senior Securities Restricted cash, current504Short-term investments41,462Financial assets:Accounts receivable6,442Contract assets1,788 Supplemental disclosure of cash flow information:Interest paid$432$Income taxes paid$—$ Total cash, cash equivalents and restricted cash cash equivalents, and short-term investments as of March31, 2025 and 2024 were $59.8million and $85.5million, respectively. See accompanying notes to the unaudited condensed consolidated financial statements. 8 Notes to Condensed Consolidated Financial Statements(Unaudited)Note 1.Description of BusinessIn these notes to the unaudited condensed consolidated financial statements, the “Company,” “we,” “us,” and “our” refers to Codexis, Note 2.Basis of Presentation and Summary of Significant Accounting PoliciesBasis of Presentation and Principles of ConsolidationThe accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally acceptedaccounting principles in the United States of America (“GAAP”) and the applicable rules and regulations of the Securities and Exchange consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K for the year ended December31, 2024.The condensed consolidated balance sheet at December31, 2024 has been derived from the audited consolidated financial statements atthat date, but does not include all disclosures, including notes, required by GAAP for complete financial statements. The significantaccounting policies used in preparation of the unaudited condensed consolidated financial statements for the three months ended March 31, policies or critical accounting estimates since December31, 2024. The unaudited condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financialstatements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of March31, 2025 and results of operations for the interim periods presented. The interim results are notnecessarily indicative of the results for any future interim period or for the entire year.The unaudited condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly-owned subsidiaries.All intercompany balances and transactions have been eliminated in consolidation. disclosure of contingent assets and liabilities. We regularly assess these estimates which primarily affect revenue recognition, deferredrevenue, inventories, valuation of equity investments, goodwill arising out of business acquisitions, accrued liabilities, stock awards, andthe valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be Short-term InvestmentsWe classify all marketable debt securities that have effective maturities of three months or less from the date of purchase as cash equivalents and those with effective maturities of greater than three months as short-term investment securities in the condensedconsolidated balance sheets. We determine the appropriate classification of our short-term investments at the time of purchase andreevaluate such designation at each balance sheet date. We have classified and accounted for our short-term investments as available-for-sale. After consideration of our risk versus reward objectives, as well as our liquidity requirements, we may sell these debt securities priorto their effective maturities. 9 in the unaudited condensed consolidated statements of operations. We determine any realized gains or losses on the sale of short-terminvestments on a specific identification method, and we record such gains and losses as a component of “Interest income” in the unauditedcondensed consolidated statements of operations. conditions specifically related to the security, the financial condition of the issuer, the Company’s intent to sell, and whether it would bemore likely than not that the Company would be required to sell the investments before the recovery of the amortized cost basis. Accounting Pronouncements Recent