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Stock-based Compensation | 9 Months Ended
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Sep. 30, 2025
Share-Based Payment Arrangement [Abstract] |
Stock-based Compensation | Stock-based Compensation Equity Incentive Plans In April 2025, our Board of Directors (the “Board”) approved the second amendment to the Codexis Inc. 2019 Incentive Award Plan, as amended (the “2019 Plan”) which amendment became effective upon stockholders' approval at the Annual Meeting of the Company’s stockholders in June 2025. The second amendment provided for an increase in the number of shares authorized and available for issuance under the 2019 Plan by 8,000,000 shares, resulting in an increase to the total shares authorized and available for issuance under the 2019 Plan from 15,897,144 shares to 23,897,144 shares. Employee Stock Purchase Plan In April 2023, our Board approved an employee stock purchase plan (as may be amended from time to time, the “ESPP”) which became effective upon approval at the 2023 Annual Meeting. The ESPP allows eligible employees of the Company to purchase shares of our common stock through payroll deductions. Offering periods are generally over a 24-month period and begin in May and November of each year. The per share purchase price will be the lower of 85% of the closing trading price per share of our common stock on the first trading date of an offering period in which a participant is enrolled or 85% of the closing trading price per share on the purchase date. Participant purchases are limited to a maximum of $25,000 of fair value of our stock per calendar year. The Company is authorized to grant up to 2,000,000 shares of common stock under the ESPP. The first offering period of the ESPP commenced in December 2023. During the three months ended September 30, 2025 and 2024, no shares of our common stock were purchased under the ESPP. For the nine months ended September 30, 2025 and 2024, 151,490 and 123,889 shares of our common stock were purchased under the ESPP, respectively. As of September 30, 2025, 1,585,353 shares of common stock were available for future issuance under the ESPP. We recognized $0.1 million and $0.3 million of stock-based compensation expenses related to the ESPP for the three and nine months ended September 30, 2025, respectively, and $0.1 million and $0.2 million for the three and nine months ended September 30, 2024, respectively. As of September 30, 2025, the total unrecognized stock-based compensation expense, net of expected forfeitures, related to the ESPP was $0.7 million and is expected to be recognized over the remaining offering period. Stock-Based Compensation Expense Stock-based compensation expense is included in the unaudited condensed consolidated statements of operations as follows (in thousands):
| Three Months Ended September 30, |  | Nine Months Ended September 30,
| 2025 |  | 2024 |  | 2025 |  | 2024
Cost of product revenue | $ | 16 |  |  | $ | 93 |  |  | $ | 134 |  |  | $ | 309 |
Research and development | 675 |  |  | 690 |  |  | 2,064 |  |  | 2,151 |
Selling, general and administrative | 1,822 |  |  | 1,925 |  |  | 5,226 |  |  | 8,101 |
Total | $ | 2,513 |  |  | $ | 2,708 |  |  | $ | 7,424 |  |  | $ | 10,561 |
The following table presents total stock-based compensation expense by security type included in the unaudited condensed consolidated statements of operations (in thousands):
| Three Months Ended September 30, |  | Nine Months Ended September 30,
| 2025 |  | 2024 |  | 2025 |  | 2024
Stock options | $ | 1,455 |  |  | $ | 1,506 |  |  | $ | 4,289 |  |  | $ | 5,137 |
Restricted stock units (“RSUs”) and RSAs | 950 |  |  | 1,109 |  |  | 2,805 |  |  | 3,578 |
Performance-contingent restricted stock units (“PSUs”) | — |  |  | — |  |  | — |  |  | 247 |
Performance based options (“PBOs”) | — |  |  | — |  |  | — |  |  | 1,357 |
ESPP | 108 |  |  | 93 |  |  | 330 |  |  | 242 |
Total | $ | 2,513 |  |  | $ | 2,708 |  |  | $ | 7,424 |  |  | $ | 10,561 |
On June 29, 2024, we entered into an Advisory Services Agreement with a former executive of the Company. Pursuant to the advisory agreement, which expired in August 2025, the exercise period for the former executive’s vested stock options and performance-based options was also extended. The modification resulted in a stock-based compensation expense of $2.0 million recognized in selling, general and administrative expenses during the nine months ended September 30, 2024. As of September 30, 2025, unrecognized stock-based compensation expense, net of expected forfeitures, was $9.7 million related to unvested stock options, and $4.5 million related to unvested RSUs and RSAs. Stock-based compensation expense for these awards will be recognized through 2029.

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