Codexis Reports 33% Revenue Decline and $19.6 Million Net Loss in Q3 2025

Codexis, Inc. reported a significant decline in financial performance for the third quarter of 2025, with total revenues of $8.6 million, down 33% from $12.8 million in the same period last year. The decrease was primarily driven by a 39% drop in product revenue, which fell to $6.8 million from $11.2 million, attributed to variability in customer manufacturing schedules and clinical trial timelines. Research and development revenue, however, saw a slight increase of 7% to $1.8 million, reflecting higher revenue from existing collaboration agreements.

In terms of profitability, Codexis recorded a net loss of $19.6 million for the third quarter, a modest improvement compared to a net loss of $20.6 million in the prior year. The loss per share was $0.22, compared to $0.29 in the same quarter of 2024. The company’s total operating expenses decreased by 6% to $27.6 million, driven by reductions in selling, general, and administrative expenses, as well as cost of product revenue. The gross margin for product revenue improved to 64%, up from 61% in the previous year, indicating a shift towards more profitable product lines.

Codexis has also made strategic moves to enhance its operational capabilities. The company recently entered into an enzyme supply assurance agreement with Merck Sharp & Dohme LLC, which is expected to generate a one-time payment of $37.8 million in the fourth quarter of 2025. Additionally, Codexis announced a workforce reduction of approximately 24% to streamline operations and focus on its ECO Synthesis platform, which is designed for the large-scale manufacture of RNA interference therapeutics. This restructuring is anticipated to incur an expense of about $3.5 million, expected to be recognized in the fourth quarter.

As of September 30, 2025, Codexis reported total assets of $124 million, a decrease from $149 million at the end of 2024. The company’s cash and cash equivalents increased to $25.4 million, up from $19.3 million, while short-term investments decreased to $33.4 million from $54.2 million. The total liabilities rose to $85.4 million, primarily due to an increase in long-term debt associated with the Innovatus Loan, which now stands at $39.7 million. The company’s working capital was reported at $57.7 million, down from $75.1 million at the end of the previous year.

Looking ahead, Codexis remains focused on leveraging its proprietary CodeEvolver technology platform to enhance its enzyme offerings and expand its market presence. The company anticipates that the recent strategic agreements and operational adjustments will position it for improved performance in the coming quarters. However, the ongoing variability in customer demand and market conditions will continue to influence its financial results.