CODEXIS INC

Rule 10b5-1 Trading Arrangements

During the three months ended March 31, 2024, none of the directors or executive officers of the Company adopted orterminated a Rule 10b5-1 trading arrangement or a “non-Rule 10b5-1 trading arrangement” (each as defined in Item 408 of Regulation S-K).

Cantor Sales Agreement

On May 2, 2024, we entered into a Controlled Equity Offering℠ Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald & Co. (“Cantor”), under which we may offer and sell, from time to time at our sole discretion, shares of our common stock, par value $0.0001 per share (the “Common Stock”), having an aggregate offering price of up to $75.0 million through Cantor, as sales agent (the “ATM Offering”).

Cantor may sell the Common Stock by any method that is deemed to be an “at the market offering” as defined in Rule 415 of the Securities Act of 1933, as amended, including sales made directly on the Nasdaq Global Select Market (“Nasdaq”) or any other trading market for the Common Stock. Cantor will use commercially reasonable efforts, consistent with its normal sales and trading practices and applicable state and federal laws, rules and regulations and the rules of Nasdaq, to sell the Common Stock from time to time, based upon instructions from us (including any price, time or size limits or other customary parameters or conditions the Company may impose). We will pay Cantor a commission of up to 3.0%of the gross sales proceeds of any Common Stock sold through Cantor under the ATM Offering and have provided Cantor with customary indemnification rights.

We are not obligated to make any sales of Common Stock under the Sales Agreement. The offering of shares of Common Stock pursuant to the Sales Agreement will terminate upon the termination of the Sales Agreement as permitted therein.

The foregoing description of the Sales Agreement is qualified in its entirety by reference to the Sales Agreement, a copy of which will be filed as an exhibit to the 2024 Registration Statement (as defined below).

The shares of Common Stock being offered pursuant to the Sales Agreement will be offered and sold pursuant to a shelf registration statement on Form S-3 (the “2024 Registration Statement”) that we intend to file with the Securities and Exchange Commission and a prospectus relating to the ATM Offering which will be included in the 2024 Registration Statement. None of our securities, including any shares of Common Stock, may be sold under the Sales Agreement, and no offers to buy such securities may be accepted, prior to the time the 2024 Registration Statement becomes effective.

The legal opinion of Sidley Austin LLP relating to the shares of Common Stock being offered pursuant to the Sales Agreement will be filed as Exhibit 5.1 to the 2024 Registration Statement.

This report shall not constitute an offer to sell or the solicitation of an offer to buy the securities discussed herein, nor shall there be any offer, solicitation, or sale of the securities in any state in which such offer, solicitation or sale would be unlawful prior to registration or qualification under the securities laws of any such state.