CODEXIS, INC.

Previous wording

The following management's discussion and analysis of our financial condition and results of operations should be read in conjunction with the unaudited condensed consolidated financial statements and the related notes thereto included elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto and management's discussion and analysis of financial condition and results of operations for the year ended December 31, 2025 included in our Annual Report on Form 10-K for the year ended December 31, 2025, as filed with the SEC on March 11, 2026 (the “Annual Report”). This Quarterly Report on Form 10-Q contains forward-looking statements within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). These statements include, but are not limited to, expectations regarding our strategy, business plans, financial performance and developments relating to our industry. These statements are often identified by the use of words such as “may,” “will,” “expect,” “believe,” “anticipate,” “intend,” “could,” “should,” “estimate,” or “continue,” and similar expressions or variations. Such forward-looking statements are subject to risks, uncertainties and other factors that could cause actual results and the timing of certain events to differ materially from future results expressed or implied by such forward-looking statements. Factors that could cause or contribute to such differences include, but are not limited to, those discussed in Part II, Item 1A: “Risk Factors” of this Quarterly Report on Form 10-Q and Part I, Item 1A: “Risk Factors” of our Annual Report, and elsewhere in this report. The forward-looking statements in this Quarterly Report on Form 10-Q represent our views as of the date of this Quarterly Report on Form 10-Q. We anticipate that subsequent events and developments may cause our views to change. However, while we may elect to update these forward-looking statements at some point in the future, we have no current intention of doing so except to the extent required by applicable law. You should, therefore, not rely on these forward-looking statements as representing our views as of any date subsequent to the date of this Quarterly Report on Form 10-Q.

Current wording

The following management's discussion and analysis of our financial condition and results of operations should be read in conjunction with the unaudited condensed consolidated financial statements and the related notes thereto included elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto and management's discussion and analysis of financial condition and results of operations for the year ended December 31, 2025 included in our Annual Report on Form 10-K for the year ended December 31, 2025, as filed with the SEC on March 11, 2026 (the “Annual Report”). This Quarterly Report on Form 10-Q contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended (the “Securities Act”), and Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). These statements include, but are not limited to, expectations regarding our strategy, business plans, financial performance and developments relating to our industry. These statements are often identified by the use of words such as “may,” “will,” “expect,” “believe,” “anticipate,” “intend,” “could,” “should,” “estimate,” or “continue,” and similar expressions or variations. Such forward-looking statements are subject to risks, uncertainties and other factors that could cause actual results and the timing of certain events to differ materially from future results expressed or implied by such forward-looking statements. Factors that could cause or contribute to such differences include, but are not limited to, those discussed in Part II, Item 1A: “Risk Factors” of this Quarterly Report on Form 10-Q and Part I, Item 1A: “Risk Factors” of our Annual Report, and elsewhere in this report. The forward-looking statements in this Quarterly Report on Form 10-Q represent our views as of the date of this Quarterly Report on Form 10-Q. We anticipate that subsequent events and developments may cause our views to change. However, while we may elect to update these forward-looking statements at some point in the future, we have no current intention of doing so except to the extent required by applicable law. You should, therefore, not rely on these forward-looking statements as representing our views as of any date subsequent to the date of this Quarterly Report on Form 10-Q.

Previous wording

Our ECO Synthesis® manufacturing platform is comprised of enzymatic tools and processes that are designed to enable large-scale manufacture of RNA interference (“RNAi”) therapeutics. We use the CodeEvolver platform technology to develop enzymes for the synthesis of RNAi therapeutics in production processes that deliver improvements, including purity, yield, and manufacturing efficiency. In November 2024, we presented data at the TIDES Europe conference demonstrating the successful end-to-end enzymatic synthesis of an entire commercially approved small interfering ribonucleic acid (“siRNA”) therapeutic asset with the ECO Synthesis manufacturing platform. In addition to using full enzymatic sequential synthesis, adding one nucleotide at a time to synthesize the two strands from beginning to end, we demonstrated synthesis of the same siRNA asset using three other routes utilizing enzymatic ligation with our double-stranded RNA (“dsRNA”) ligase, which can stitch together fragments of chemically and/or enzymatically synthesized RNA to form the full siRNA drug structure. For the three other routes, our data highlighted that full-length oligonucleotides of equal quality and yields were obtained whether the fragments were made with enzymes or by traditional solid phase oligonucleotide synthesis (“SPOS”) (current standard production route for oligonucleotide manufacturing). At the end of 2024, we completed the build out of our ECO Synthesis Innovation Lab, a facility where our ECO Synthesis manufacturing platform is deployed to synthesize gram-scale quantities of a customer’s desired siRNA construct suitable for pre-clinical testing. In addition, the infrastructure allows us to provide process development, analytical method development and other manufacturing process optimization which is required to enable the siRNA to proceed to clinical-stage manufacturing and testing. In 2025, we successfully manufactured non-good manufacturing practice (“GMP”)-grade siRNA drug substance for customers in our Innovation Lab under development services contracts. We also entered into partnerships with three large-scale contract development and manufacturing organizations (“CDMOs”)to evaluate our ECO platform of enzymatic tools and processes to ultimately synthesize GMP-grade siRNA drug substance for our customers. In each of these agreements, we are currently in the feasibility testing stage and expect to advance at least one of these partnerships, including initiating a technology transfer to that organization, in 2026. We believe these relationships to be a vital extension of our strategy to be a technology solutions provider for our customers. Through these arrangements, our customers will have access to proven, large-scale commercial manufacturers who are familiar with our process, who can then offer a seamless manufacturing scale-up of our customers’ products. We expect to expand our enzymatic tools and process offerings as we further enhance the ECO Synthesis platf…

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Current wording

At the end of 2024, we completed the build out of our ECO Synthesis Innovation Lab, a facility where our ECO Synthesis manufacturing platform is deployed to synthesize gram-scale quantities of a customer’s desired siRNA construct suitable for pre-clinical testing. In addition, the infrastructure allows us to provide process development, analytical method development and other manufacturing process optimization which is required to enable the siRNA to proceed to clinical-stage manufacturing and testing. In 2025, we successfully manufactured non-good manufacturing practice (“GMP”)-grade siRNA drug substance for customers in our Innovation Lab under development services contracts. We also entered into partnerships with three large-scale contract development and manufacturing organizations (“CDMOs”)to evaluate our ECO platform of enzymatic tools and processes to ultimately synthesize GMP-grade siRNA drug substance for our customers. Under each of these agreements, we have conducted technology transfer to several partners in 2026 for further evaluation of the technology. We believe these relationships to be a vital extension of our strategy to be a technology solutions provider for our customers. Through these arrangements, our customers will have access to proven, large-scale commercial manufacturers who are familiar with our process, who can then offer a seamless manufacturing scale-up of our customers’products. We expect to expand our enzymatic tools and process offerings as we further enhance the ECO Synthesis platform to address the overall market needs for scalable and sustainable RNAi manufacturing.

Previous wording

Cost of product revenue decreased by $0.7 million in the three months ended March 31, 2026, compared to the same period in 2025. Product gross margin was 71% in the three months ended March 31, 2026, compared to 55% in the corresponding period in 2025. The changes in cost of product revenue and product gross margins are primarily due to a shift in sales toward more profitable products, and declines in less profitable legacy products.

Current wording

Cost of product revenue increased by $1.4 million and$0.7 millionin the three and six months ended June 30, 2026, respectively, compared to the same period in 2025. Product gross margin was 73% and 73% in the three and six months ended June 30, 2026, respectively, compared to 72% and 64%in the corresponding period in 2025. The changes in cost of product revenue and product gross margins are primarily due to a shift in sales toward more profitable products, and declines in less profitable legacy products.

Previous wording

Selling, general and administrative expenses decreased by $2.6 million during the three months ended March 31, 2026, compared to the same period in 2025 primarily due to $3.1 million decrease in employee-related costs due to lower headcount, $0.3 million in lower consulting and outside services, $0.5 million in lower legal costs,$1.0 million in lower stock-based compensation expenses, partially offset by a $2.3 million increase in higher allocable costs.

Current wording

Selling, general and administrative expenses decreased by $1.4 million during the three months ended June 30, 2026, compared to the same period in 2025 primarily due to$0.8 million in lower stock-based compensation expenses, $0.6 million decrease in employee-related costs due to lower headcount, $0.2 million decrease in allocable costs and$0.1 million in lower consulting and outside services, partially offset by$0.2 million increase in facilities associated costs. The decrease in selling, general and administrative expenses of $4.0 million during the six months ended June 30, 2026 as compared to the same period in 2025, was primarily due to $2.0 million in lower employee-related costs, $1.6 million decrease in stock-based compensation expense, $0.5 million in lower legal costs, $0.2 million decrease in consulting and outside services and $0.2 million in lower allocable costs, partially offset by a $0.4 million increase in facilities associated costs.

Previous wording

Interest and other expense, net increased by $0.3 million in the three months ended March 31, 2026, compared to the same period in 2025, primarily due to higher interest related to long-term debt due to the funding of the second tranche of the Innovatus Loan in June 2025.

Current wording

Interest and other expense, netincreased by $0.3 million and$0.7 million in the three and six months ended June 30, 2026, respectively, compared to the same period in 2025, primarily due to higher interest related to long-term debt due to the funding of the second tranche of the Innovatus Loan in June 2025.

Previous wording

The provision for income taxes for the three months ended March 31, 2026 was primarily due to income taxes imposed by foreign taxing authorities related to the ongoing liquidation of our Indian subsidiary. The provision for income taxes for the three months ended March 31, 2025 was primarily due to the accrual of interest and penalties on historic uncertain tax positions.

Current wording

The provision for income taxes for the three and six months ended June 30, 2026 was primarily due to income taxes imposed by foreign taxing authorities related to the ongoing liquidation of our Indian subsidiary and accrual of interest and penalties on historic uncertain tax positions. The provision for income taxes for thethree and six months ended June 30, 2025 was primarily due to the accrual of interest and penalties on historic uncertain tax positions.

Previous wording

Net loss for the three months ended March 31, 2026 was $8.7 million, or a net loss per basic and diluted share of $0.10. This compared to a net loss of $20.7 million, or a net loss per basic and diluted share of $0.25, for the three months ended March 31, 2025. The decrease in net loss was primarily related to$7.7 million higher revenue and$4.7 million lower costs and operating expenses.

Current wording

Net loss for the three months ended June 30, 2026 was $12.0 million, or a net loss per basic and diluted share of $0.13. This compared to a net loss of $13.3 million, or a net loss per basic and diluted share of $0.16, for the three months ended June 30, 2025. The decrease in net loss was primarily related to$2.0 million lower costs and operating expenses in 2026.

Previous wording

Our primary uses of capital for the foreseeable future, including the next 12 months, are for compensation and related expenses, research and development expenses including manufacturing costs, laboratory and related supplies, legal and other outside services, and general overhead costs.

Current wording

Our primary uses of capital for the foreseeable future, including the next 12 months, are for compensation and related expenses, research and development expenses including manufacturing costs, laboratory and related supplies, legal and other outside services, general overhead costs, and capital expenditures associated with our planned facility buildout and related equipment purchases.

Previous wording

We have historically experienced negative cash flows from operations as we continue to invest in key technology development projects and improvements to our CodeEvolver technology platform, develop and commercialize new and existing products including our ECO Synthesis manufacturing platform and expand our business development and collaboration with new customers. Our cash flows from operations will continue to be affected principally by product sales and product gross margins, sales from licensing our technology to major pharmaceutical companies, and collaborative research and development services provided to customers, as well as our headcount costs. Our primary source of cash flows from operating activities is cash receipts from our customers for purchases of products, collaborative research and development services, and licensing our technology to major pharmaceutical companies. Our largest uses of cash from operating activities are for employee-related expenditures, rent payments, inventory purchases to support our product sales and non-payroll research and development costs.

Current wording

We have historically experienced negative cash flows from operations as we continue to invest in key technology development projects and improvements to our CodeEvolver technology platform, develop and commercialize new and existing products including our ECO Synthesis manufacturing platform and expand our business development and collaboration with new customers. Our cash flows from operations will continue to be affected principally by product sales and product gross margins, sales from licensing our technology to major pharmaceutical companies, and collaborative research and development services provided to customers, as well as our headcount costs. Our primary source of cash flows from operating activities is cash receipts from our customers for purchases of products, collaborative research and development services, and licensing our technology to major pharmaceutical companies. Our largest uses of cash from operating activities are for employee-related expenditures, rent payments, inventory purchases to support our product sales and non-payroll research and development costs. In addition, we expect capital expenditures to increase as we continue investments in our new manufacturing facility, including facility improvements and equipment purchases necessary to support future operations.

Previous wording

On May 2, 2024, we entered into the Cantor Sales Agreement with Cantor, under which Cantor, at our discretion and at such times that we may determine from time to time, may sell up to a maximum of $75.0 million of shares of our common stock. Under the terms of the Cantor Sales Agreement, Cantor may sell the shares at market prices by any method that is deemed to be an “at the market offering” as defined in Rule 415 under the Securities Act. On May 2, 2024, we filed a registration statement on Form S-3 registering the offer and sale of these shares under the Securities Act which became effective on May 14, 2024. We will pay a commission of up to 3.0%of gross sales proceeds of any common stock sold under the Cantor Sales Agreement. In 2024, 10,440,000 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement, all during the third quarter of 2024, and we received net proceeds of $29.7 million after Cantor’s commissions and direct offering expenses. In 2025, 7,244,966 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement, all during the second quarter of 2025, and we received $16.4 million in net proceeds after Cantor’s commissions and direct offering expenses. As of March 31, 2026, $26.4 million of shares remained available for sale under the Cantor Sales Agreement.

Current wording

On May 2, 2024, we entered into the Cantor Sales Agreement with Cantor, under which Cantor, at our discretion and at such times that we may determine from time to time, may sell up to a maximum of $75.0 million of shares of our common stock. Under the terms of the Cantor Sales Agreement, Cantor may sell the shares at market prices by any method that is deemed to be an “at the market offering” as defined in Rule 415 under the Securities Act. On May 2, 2024, we filed a registration statement on Form S-3 registering the offer and sale of these shares under the Securities Act which became effective on May 14, 2024. We will pay a commission of up to 3.0%of gross sales proceeds of any common stock sold under the Cantor Sales Agreement. In 2024, 10,440,000 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement, all during the third quarter of 2024, and we received net proceeds of $29.7 million after Cantor’s commissions and direct offering expenses. In 2025, 7,244,966 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement, all during the second quarter of 2025, and we received $16.4 million in net proceeds after Cantor’s commissions and direct offering expenses. As of June 30, 2026, $26.4 million remained available for sale under the Cantor Sales Agreement.

Previous wording

The following is a summary of cash flows for the three months ended March 31, 2026 and 2025 (in thousands):

Current wording

The following is a summary of cash flows for the six months ended June 30, 2026 and 2025 (in thousands):

Previous wording

The $0.6 million decrease in net cash used in operating activities for the three months ended March 31, 2026 as compared to the same period in 2025, was primarily due to smaller net operating loss driven by higher revenue and lower operating expenses, including decreased employee-related costs resulting from the reduction in force implemented in the fourth quarter of 2025, as well as lower spending on outside services.

Current wording

The $9.0 million decrease in net cash used in operating activities for the six months ended June 30, 2026 as compared to the same period in 2025, was primarily due to smaller net operating loss driven by higher revenue and lower operating expenses, including decreased employee-related costs resulting from the reduction in force implemented in the fourth quarter of 2025, as well as lower spending on outside services.

Previous wording

The $12.9 million decrease in net cash provided by investing activities for the three months ended March 31, 2026 as compared to the same period in 2025, was primarily due to higher purchases of short-term investments and lower proceeds from maturities of short-term investments in the current period, partially offset by reduced capital expenditures.

Current wording

The $12.3 million decrease in net cash provided by investing activities for the six months ended June 30, 2026 as compared to the same period in 2025, was primarily due to higher purchases of short-term investments and lower proceeds from maturities of short-term investments in the current period, partially offset by reduced capital expenditures.

Previous wording

The $1.1 million decrease in net cash provided by financing activities for the three months ended March 31, 2026 as compared to the same period in 2025, was primarily due to the absence of proceeds from employee stock option exercises in the current period.

Current wording

The $27.8 million decrease in net cash provided by financing activities for the six months ended June 30, 2026 as compared to the same period in 2025, was primarily due to the absence of proceeds from issuance of common stock in connection with an equity sales agreement and proceeds from long term debt in the current period.

Previous wording

The preparation of financial statements in conformity with generally accepted accounting principles requires management to make judgments, estimates and assumptions in the preparation of our consolidated financial statements and accompanying notes. Actual results could differ from those estimates. There have been no material changes to our critical accounting policies or estimates during the three months ended March 31, 2026 from those discussed in our Annual Report.

Current wording

The preparation of financial statements in conformity with generally accepted accounting principles requires management to make judgments, estimates and assumptions in the preparation of our consolidated financial statements and accompanying notes. Actual results could differ from those estimates. There have been no material changes to our critical accounting policies or estimates during the three and six months ended June 30, 2026 from those discussed in our Annual Report.