Yield10 Bioscience : 2024 Special Meeting of Stockholders

April 2, 2024

Dear Stockholder:

You are cordially invited to attend a special meeting (the "Special Meeting") of stockholders of Yield10 Bioscience, Inc. (the "Company"), to be held at 9:00 a.m. Eastern Time on April 26, 2024, in virtual-only format.

We will hold the Special Meeting virtually via live audio webcast on the Internet. We believe hosting a virtual meeting enables greater stockholder attendance and participation from any location around the world, improves meeting efficiency and our ability to communicate effectively with our stockholders, and reduces the cost and environmental impact of the Special Meeting. You will be able to attend the Special Meeting, vote and submit your questions during the meeting by pre-registering at https://viewproxy.com/yield10bio/2024/. You will not be able to attend the Special Meeting in person.

Details regarding the Special Meeting, the business to be conducted at the Special Meeting, and

information about the Company that you should consider when you vote your shares are described in this proxy statement. You may obtain additional information about the Company from documents we file with the Securities and Exchange Commission.

At the Special Meeting, we will ask stockholders to approve:

1. A proposed amendment to the Yield10 Bioscience, Inc. Amended and Restated Certificate of Incorporation, as amended, to effect a reverse stock split of our issued and outstanding shares of common stock, at a ratio of between 1-for-5 and 1-for-25 ("Proposal 1"); and
2. Adjournment of the Special Meeting, if necessary, if a quorum is present, to solicit additional proxies if there are not sufficient votes in favor of Proposal 1 ("Proposal 2").

The Board of Directors recommends that you vote "FOR" each of these proposals.

We hope you will be able to attend the Special Meeting. Whether or not you plan to attend the Special Meeting, we urge you to complete, sign, date and mail promptly the enclosed proxy which is being solicited on behalf of the Board of Directors so that your shares will be represented at the Special Meeting. A return envelope, which requires no postage if mailed in the United States, is enclosed for that purpose. You need to vote in accordance with the instructions listed on the proxy card. If shares are held in a bank or brokerage account, you may be eligible to vote electronically or by telephone. Please refer to the enclosed voting instruction form for instructions. If you attend the Special Meeting, you may vote during the live webcast, provided that you have registered at https://viewproxy.com/yield10bio/2024/, even if you have previously returned your proxy card. Your prompt cooperation will be greatly appreciated.

Sincerely,

Oliver P. Peoples

President and Chief Executive Officer

YIELD10 BIOSCIENCE, INC.

19 Presidential Way

Woburn, Massachusetts 01801

(617) 583-1700

NOTICE OF SPECIAL MEETING OF STOCKHOLDERS

TIME: 9:00 a.m. Eastern Time

DATE: April 26, 2024

MEETING FORMAT: The Special Meeting will be a virtual meeting via live audio webcast on the Internet. Stockholders who wish to attend the Special Meeting must pre-register at https://viewproxy.com/yield10bio/2024/by 11:59 p.m.Eastern Time, on April 25, 2024. You will receive an event passcode to attend the meeting, and a virtual control number to vote if proper documentation is provided. The live audio webcast of the Special Meeting can be accessed by stockholders on the day of the meeting by clicking on the link you have received in your e-mail confirmations. You will not be able to attend the Special Meeting in person.

We believe hosting a virtual meeting enables greater stockholder attendance and participation from any location around the world, improves meeting efficiency and our ability to communicate effectively with our stockholders. It also reduces the cost and environmental impact of the Special Meeting. Both stockholders of record and street name stockholders will be able to attend the Special Meeting via live audio webcast, submit their questions during the meeting and vote their shares electronically at the Special Meeting.

There will be technicians ready to assist you with any technical difficulties you may have accessing the Special Meeting live audio webcast. Please be sure to check in by 8:30 a.m. Eastern Time, on April 26, 2024 (at least 15 minutes prior to the start of the meeting is recommended) the day of the meeting, so that any technical difficulties may be addressed before the Special Meeting live audio webcast begins. If you encounter any difficulties accessing the webcast during the check-in or meeting time, please email virtualmeeting@viewproxy.com or call 866-612-8937.

PURPOSE: To approve:

1. A proposed amendment to the Yield10 Bioscience, Inc. Amended and Restated Certificate of Incorporation, as amended (the "Certificate of Incorporation"), to effect a reverse stock split of our issued and outstanding shares of common stock, at a ratio of between 1-for-5 and 1-for-25 ("Proposal 1"); and
2. Adjournment of the Special Meeting, if necessary, if a quorum is present, to solicit additional proxies if there are not sufficient votes in favor of Proposal 1 ("Proposal 2").

WHO MAY VOTE:

Only stockholders of record at the close of business on April 1, 2024, are entitled to notice of and to vote at the Special Meeting and at any adjournment or postponement thereof.

All stockholders are cordially invited to attend the Special Meeting. However, to assure your representation at the Special Meeting, we urge you, whether or not you plan to attend the Special Meeting, to complete, sign, date and mail promptly the enclosed proxy card, which is being solicited on behalf of the Board of Directors so that your shares will be represented at the Special Meeting. A return envelope which requires no postage if mailed in the United States is enclosed for that purpose. You need to vote in accordance with the instructions listed on the proxy card. If shares are held in a bank or brokerage account, you may be eligible to vote electronically or by telephone. Please refer to the enclosed voting instruction form for instructions. If you attend the Special Meeting, you may vote during the live webcast, provided that you have registered at https://viewproxy.com/yield10bio/2024/ even if you have previously returned your proxy card.

BY ORDER OF THE BOARD OF DIRECTORS

Lynne H. Brum

Secretary

WHETHER OR NOT YOU EXPECT TO ATTEND THE SPECIAL MEETING, PLEASE COMPLETE, SIGN, DATE AND MAIL PROMPTLY THE ENCLOSED PROXY CARD WHICH IS BEING SOLICITED ON BEHALF OF THE BOARD OF DIRECTORS SO THAT YOUR SHARES WILL BE REPRESENTED AT THE SPECIAL MEETING. A RETURN ENVELOPE, WHICH REQUIRES NO POSTAGE IF MAILED IN THE UNITED STATES, IS ENCLOSED FOR THAT PURPOSE. YOU NEED TO VOTE IN ACCORDANCE WITH THE INSTRUCTIONS LISTED ON THE PROXY CARD. IF SHARES ARE HELD IN A BANK OR BROKERAGE ACCOUNT, YOU MAY BE ELIGIBLE TO VOTE ELECTRONICALLY OR BY TELEPHONE. PLEASE REFER TO THE ENCLOSED VOTING INSTRUCTION FORM FOR INSTRUCTIONS.

PRELIMINARY COPIES FILED PURSUANT TO RULE 14a-6(a)

YIELD10 BIOSCIENCE, INC.

19 Presidential Way

Woburn, Massachusetts 01801

PROXY STATEMENT FOR THE YIELD10 BIOSCIENCE, INC.

SPECIAL MEETING OF STOCKHOLDERS TO BE HELD ON April 26, 2024

This proxy statement, along with the accompanying Notice of the Special Meeting of Stockholders, contains information about the Special Meeting of Stockholders of Yield10 Bioscience, Inc., including any adjournments or postponements thereof (the "Special Meeting"). We are holding the Special Meeting at 9:00 a.m. Eastern Time, on April 26, 2024 in a virtual format. You may attend the Special Meeting by accessing the link provided in your email confirmation when you registered.

In this proxy statement, we refer to Yield10 Bioscience, Inc. as "Yield10," "Yield10 Bioscience," "the Company," "we" and "us."

This proxy statement relates to the solicitation of proxies by our Board of Directors for use at the Special Meeting.

On or about April 3, 2024, we intend to begin sending this proxy statement, the attached Notice of Special Meeting of Stockholders and the enclosed proxy card to all stockholders entitled to vote at the Special Meeting.

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YIELD10 BIOSCIENCE, INC.

19 Presidential Way

Woburn, Massachusetts 01801

PROXY STATEMENT

For a Special Meeting of Stockholders

To Be Held on April 26, 2024

Proxies in the form enclosed with this proxy statement are solicited by the Board of Directors of Yield10 Bioscience, Inc., a Delaware corporation ("Yield10" or the "Company"), for use at the Special Meeting of Stockholders of Yield10 to be held on April 26, 2024, at 9:00 a.m., Eastern Time, or at any adjournments or postponements thereof (the "Special Meeting") in virtual-only format at https://viewproxy.com/yield10bio/2024/.

The purpose of the Special Meeting is to ask stockholders to approve:

1. A proposed amendment to our Certificate of Incorporation to effect a reverse stock split of our issued and outstanding shares of common stock, at a ratio of between 1-for-5 and 1-for-25 ("Proposal 1"); and
2. Adjournment of the Special Meeting, if necessary, if a quorum is present, to solicit additional proxies if there are not sufficient votes in favor of Proposal 1 ("Proposal 2").

Only stockholders of record at the close of business on April 1, 2024 (the "Record Date") will be entitled to receive notice of and to vote at the Special Meeting. As of the Record Date, 15,401,706 shares of common stock were issued, outstanding and entitled to vote.

VOTING AND OTHER INFORMATION

How Do I Attend the Special Meeting?

The Special Meeting will be held in a virtual meeting format only, with no physical in-person meeting. The Special Meeting will be held via live audio webcast on the Internet on April 26, 2024, starting at 9:00 a.m. Eastern Time. We have designed our virtual format to enhance, rather than constrain stockholder access, participation and communication. Stockholders may attend the Special Meeting by registering at https://viewproxy.com/yield10bio/2024/. Stockholders may vote and submit questions while connected to the Special Meeting. You need not attend the Special Meeting in order to vote.

In order to attend the Special Meeting, you must register in advance at https://viewproxy.com/yield10bio/2024/ prior to the deadline of April 25, 2024 at 11:59 p.m. Eastern Time. Upon completing your registration, you will receive further instructions via email, including your unique link that will allow you to access the Special Meeting, vote online during the Special Meeting and will permit you to submit questions during the Special Meeting. You will also be permitted to submit questions at the time of registration. You may ask questions that are confined to matters properly presented at the Special Meeting and of general Company concern. The live audio webcast of the Special Meeting can be accessed by stockholders on the day of the meeting at https://viewproxy.com/yield10bio/2024/.

The Special Meeting will begin promptly at 9:00 a.m. Eastern Time. We encourage you to access the Special Meeting prior to the start time. Please be sure to check in by 8:30 a.m. Eastern Time, on April 26, 2024 (at least 15 minutes prior to the start of the meeting is recommended) the day of the meeting, so that any technical difficulties may be addressed before the Special Meeting live audio webcast begins. We recommend that you carefully review the procedures needed to gain admission in advance. There will be technicians ready to assist you with any technical difficulties you may have accessing the Special Meeting live audio webcast. If you encounter any difficulties accessing the webcast during the check-in or meeting time, please email virtualmeeting@viewproxy.com or call 866-612-8937.

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Who May Vote?

The holders of common stock are entitled to one vote per share on any proposal to be presented at the Special Meeting. Stockholders may vote during the live webcast, provided that they have registered at https://viewproxy.com/yield10bio/2024/, or by proxy. Stockholders may vote by proxy by completing, signing, dating and returning the accompanying proxy card in the prepaid postage envelope enclosed for that purpose in accordance with the instructions listed on the proxy card. Execution of a proxy will not in any way affect a stockholder's right to attend the Special Meeting and vote during the live webcast.

Any proxy given pursuant to this solicitation may be revoked by the person giving it any time before the taking of the vote at the Special Meeting. Proxies may be revoked by (1) filing with the Secretary of Yield10, before the taking of the vote at the Special Meeting, a written notice of revocation bearing a later date than the proxy, (2) duly executing a later-dated proxy relating to the same shares and delivering it to the Secretary of Yield10, in accordance with the instructions listed on the proxy card, before the taking of the vote at the Special Meeting, (3) if shares are held in a bank or brokerage account and if eligible, by transmitting a subsequent vote over the Internet or by telephone, or (4) attending the Special Meeting and voting during the live webcast, provided that you have registered at https://viewproxy.com/yield10bio/2024/, after which you will receive further instructions via email, including your unique link that will allow you access to the special meeting and to submit questions during the special meeting (although attendance at the Special Meeting will not in and of itself constitute a revocation of a proxy). Any written notice of revocation or subsequent proxy should be sent to Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, Attention: Secretary, so as to be delivered before the taking of the vote at the Special Meeting. Telephone and Internet voting facilities for stockholders of record will be available 24 hours a day and will close at 11:59 p.m. Eastern Time on April 25, 2024.

If your shares are registered in your name with our transfer agent, Equiniti Trust Company, LLC, or if you have stock certificates, they will not be counted if you do not vote as described above. If your shares are held by a broker on your behalf (that is, in "street name"), you may be required to present an account statement or letter from your bank or brokerage firm showing that you are the beneficial owner of the shares as of the Record Date in order to be admitted to the Special Meeting. To be able to vote your shares held in street name at the Special Meeting, you will need to obtain a proxy from the holder of record.

The persons named as attorneys-in-fact in the proxies, Oliver P. Peoples and Charles B. Haaser, were selected by the Board of Directors and are officers of the Company. All properly executed proxies returned in time to be counted at the Special Meeting will be voted by such persons at the Special Meeting as stated below. When a choice has been specified on the proxy with respect to a matter, the shares represented by the proxy will be voted in accordance with the specifications. If a proxy is submitted without giving voting instructions, such shares will be voted in accordance with the Board of Directors' recommendation as noted below.

The Board of Directors recommends that you vote "FOR" each of Proposal 1 and Proposal 2.

The representation in person or by proxy of at least a majority of the outstanding shares of common stock entitled to vote at the Special Meeting is necessary to constitute a quorum for the transaction of business. Abstentions are counted as present or represented for purposes of determining the presence or absence of a quorum for the Special Meeting, and will have no effect with respect to the voting results for Proposal 1 or Proposal 2.

Under applicable exchange rules, brokers, banks and other securities intermediaries may use their discretion to vote your "uninstructed" shares with respect to matters considered to be "routine." Proposals 1 and 2 are considered to be "routine" matters under such rules, meaning that if you do not return voting instructions to your broker, bank or other agent by its deadline, your shares may be voted by your broker, bank or other agent in its discretion on Proposal 1 or Proposal 2. As such, if your shares are held in street name, and you do not instruct the broker as to how to vote your shares on Proposal 1 or Proposal 2, the broker will have discretion to vote for or against either or both proposals. If a broker chooses not to exercise such discretion, this would result in a broker "non-vote", although we do not anticipate any broker non- votes, and such broker non-votes will have no effect on the results of either Proposal. Please vote your proxy

so your vote can be counted.

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Why is the Company seeking approval for these proposals?

Proposal 1. Reverse Stock Split. On September 25, 2023, we received a notification letter from the Listing Qualifications Department of The Nasdaq Stock Market ("Nasdaq") informing us that for the prior 30 consecutive business days, the bid price of our securities had closed below $1.00 per share as required by Nasdaq Listing Rule 5550(a)(2) (the "Minimum Bid Price Requirement"). This notice had no immediate effect on our Nasdaq listing, and we were given 180 calendar days, or until March 25, 2024, to regain compliance.

On February 6, 2024, we participated in a hearing before the Nasdaq Hearings Panel, subsequent to which we were granted an extension until May 13, 2024, subject to certain conditions, to regain compliance with the Minimum Bid Price Requirement.

As of March 26, 2024, we had not regained compliance with the Minimum Bid Price Requirement since the closing bid price of our securities was not at least $1.00 per share for a minimum of ten consecutive business days. To cure the deficiency, we intend to conduct the reverse stock split of our common stock for which we are seeking stockholder approval in this proxy statement. On April 1, 2024, the closing price of our common stock as reported on Nasdaq was $0.38 per share.

The Board of Directors has approved the reverse stock split as a potential means of increasing the share price of our common stock and may choose to implement it if other options are unavailable, undesirable or insufficient. Our Board of Directors believes that maintaining our listing on Nasdaq may provide a broader market for our common stock and facilitate the use of our common stock in financing and other transactions. We expect the reverse stock split, if effected, to facilitate the continuation of such listing. We cannot assure you, however, that the reverse stock split, if effected, will result in an increase in the per share price of our common stock, or if it does, how long the increase would be sustained, if at all. Although the reverse stock split is designed to raise the stock price, there is no guarantee that the share price will rise proportionately to the reverse stock split, so the end result could be a loss of value.

We currently have 60,000,000 authorized shares of common stock. The approval of the reverse stock split will result in a lower number of issued and outstanding shares as compared to the number of our authorized shares, which would provide additional shares available for use as the Board of Directors deems appropriate or necessary.

If our stockholders approve Proposal 1, the Board of Directors in its sole discretion will determine

whether to effect the reverse stock split, no later than July 31, 2024. For more information, see "Proposal 1" contained elsewhere in this proxy statement.

Proposal 2. Adjournment of Special Meeting. We may determine that an adjournment of the Special Meeting is necessary to solicit additional proxies if there are not sufficient votes in favor of Proposal 1.For more information, see "Proposal 2" contained later in this proxy statement.

What are the costs of soliciting these proxies?

We will pay all of the costs of soliciting these proxies. In addition, our directors and employees may solicit proxies in person or by telephone or email. We will pay these employees and directors no additional compensation for these services. We will ask banks, brokers and other institutions, nominees and fiduciaries to forward these proxy materials to their principals and to obtain authority to execute proxies. We will then reimburse them for their expenses. If Yield10 does retain a proxy solicitation firm, Yield10 would pay such firm's customary fees and expenses, which fees would be expected not to exceed $15,000 plus expenses.

Vote Required

Proposal 1: Reverse Stock Split. The affirmative vote of a majority of votes cast affirmatively or negatively on this proposal is required to approve the amendment to our Certificate of Incorporation to effect a reverse stock split of our common stock. Abstentions have no effect on the vote for this proposal. Brokerage firms will have authority to vote customers' unvoted shares held by the firms in street name on this proposal. If that authority is not exercised, any resulting broker non-votes will have no effect on the vote for this proposal.

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Proposal 2. Adjournment of Special Meeting. The affirmative vote of a majority of votes cast affirmatively or negatively on this proposal is required to approve the adjournment of the Special Meeting. Abstentions will have no effect on the results of this vote. Brokerage firms will have authority to vote customers' unvoted shares held by the firms in street name on this proposal. If that authority is not exercised, any resulting broker non-votes will have broker non-votes will have no effect on the results of the vote.

Where Can I Find the Voting Results of the Special Meeting?

The preliminary voting results will be announced at the Special Meeting, and we will publish preliminary, or final results if available, in a Current Report on Form 8-K within four business days of the Special Meeting. If final results are unavailable at the time we file the Form 8-K, then we will file an amended report on Form 8-K to disclose the final voting results within four business days after the final voting results are known.

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SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table sets forth certain information with respect to the beneficial ownership of our common stock as of March 28, 2024 for (a) our named executive officers, (b) our directors, (c) our executive officers and directors as a group, and (d) each stockholder known to us to beneficially own more than five percent of our common stock. Beneficial ownership is determined in accordance with the rules of the SEC and includes voting or investment power with respect to the securities. We deem shares that may be acquired by an individual or group within 60 days following March 28, 2024, pursuant to the exercise of options or warrants to be outstanding for the purpose of computing the percentage ownership of such individual or group, but not for the purpose of computing the percentage ownership of any other person shown in the table. Except as otherwise indicated, we believe that the stockholders named in the table have sole voting and investment power with respect to all shares shown to be beneficially owned by them based on information provided to us by these stockholders. Percentage ownership is based on a total of 15,401,706 shares of our common stock issued and outstanding on March 28, 2024. Unless otherwise noted below, the address of each person listed on the table is c/o Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801.

• Less than 1.0%.

1. Beneficial ownership, as such term is used herein, is determined in accordance with Rule 13d-3(d)(1) promulgated under the Securities Exchange Act of 1934, as amended, and includes voting and/or investment power with respect to shares of our common stock. Unless otherwise indicated, the named person possesses sole voting and investment power with respect to the shares.
2. Consists of shares of common stock subject to stock options and warrants held by the person that are currently vested or will vest within 60 days after March 28, 2024.
3. Percentages of ownership are based upon 15,401,706 shares of common stock issued and outstanding as of March 28, 2024. Shares of common stock that may be acquired pursuant to options and warrants that are vested and exercisable within 60 days after March 28, 2024, are deemed outstanding for computing the percentage ownership of the person holding such options, but are not deemed outstanding for the percentage ownership of any other person.
4. The reported securities consist of 1,566,956 shares of common stock and 1,494,945 shares of common

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stock underlying the warrants owned by the JWS Living Trust, 33,999 shares of common stock owned by the Schuler Education Foundation, and 21 shares of common stock owned by the Renate Schuler Trust. Mr. Schuler has sole voting and investment power over the shares issued to the JWS Living Trust, the Schuler Family Foundation and Renate Schuler Trust. Beneficial ownership information for Mr. Schuler has been derived from his historical SEC filings.

1. Includes 31,672 shares held for Ms. Brum in the Company's 401(k) plan.
2. Includes 35,873 shares held for Dr. Peoples in the Company's 401(k) plan.
3. Includes 31,996 shares held for Dr. Snell in the Company's 401(k) plan.
4. Includes 20 shares owned by the estate of Dr. Sinskey's spouse and 4 shares owned by a trust over which Dr. Sinskey may be deemed to share voting and investment power. Dr. Sinskey disclaims beneficial ownership of such shares.
5. Includes Charles B. Haaser, who is an executive officer but not a named executive officer. Also includes a total of 30,559 shares held for Mr. Haaser in the Company's 401(k) plan.

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