BIOAMBER INC. SECOND AMENDMENT TO THE AMENDED AND RESTATED SHAREHOLDERS AGREEMENT

Exhibit 4.4

BIOAMBER INC.

SECOND AMENDMENT

TO THE AMENDED AND RESTATED SHAREHOLDERS’ AGREEMENT

THIS SECOND AMENDMENT TO THE AMENDED AND RESTATED SHAREHOLDERS’ AGREEMENT (this “Amendment”), entered into as of February 6^th, 2012, by and among BIOAMBER INC., a Delaware corporation (the “Corporation”), and the undersigned Security Holders (as defined in the Shareholders Agreement defined below).

R E C I T A L S

WHEREAS, the Corporation and certain parties identified on the signature pages thereto are parties to that certain Amended and Restated Shareholders Agreement dated as of April 15, 2011, as amended on November 4, 2011 (the “Shareholders Agreement”);

WHEREAS, pursuant to its Section 12.5, the Shareholders Agreement may be amended or otherwise modified by an instrument in writing executed by (i) the Corporation, (ii) the Shareholders holding a majority of the then outstanding Shares of the Corporation, and (iii) the Investors representing an Investor Super-Majority, as such terms are defined in the Shareholders Agreement (the “Requisite Consent”);

WHEREAS, upon execution of this Amendment, the Requisite Consent shall have been received, and this Amendment shall be binding upon the Corporation and all Security Holders who are parties to the Shareholders Agreement;

WHEREAS, the Security Holders who are parties to this Amendment believe that it is in their best interests to amend the terms and conditions of the Shareholders Agreement as set out in this Amendment; and

WHEREAS, the Corporation has agreed to be a party to this Amendment in order to acknowledge the amendment to certain rights conferred upon the Security Holders in the Shareholders Agreement.

NOW, THEREFORE, in consideration of the premises and mutual covenants set forth herein, it is mutually agreed by and among the parties as follows:

A G R E E M E N T

“Investor” – means each of (i) Sofinnova, so long as it or its Affiliates hold at least 30,000 Shares, (ii) Naxos, so long as it or its Affiliates hold at least 30,000

Shares, (iii) Mitsui CVP and Mitsui & Co., so long as they and their respective Affiliates collectively hold at least 20,000 Shares, (iv) LanxessCorporation, so long as it holds at least 5,000 Shares, and (v) Cliffton Equities Inc., so long as it holds at least 6,000 Shares.

Notwithstanding anything else set forth herein, a majority of the Directors who are nominated pursuant to paragraphs (a), (b), (c), (d) and (f) above shall have the authority to replace any of the Directors appointed pursuant to paragraph (e) above.

Expenses Reimbursement; Conflicts of Interest. The Corporation shall pay the reasonable out-of-pocket expenses (including business class air fare and other travel expenses) incurred by each director and Observer in

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connection with attending the meetings of the Board and any committee thereof (including with respect to any Subsidiary). Each of the members of the Board of the Corporation that are not employees of the Corporation (the “Non-Employee Directors”) shall be treated equally with respect to all matters, including without limitation, expense reimbursement, share options or share grants, benefits and access to Corporation information and management; provided, however, that nothing herein shall be deemed to waive or modify any information or other rights that any Investor may have pursuant to the terms of this or any other agreement with the Corporation. The parties acknowledge that one or more of the Investors (including, for the avoidance of doubt, Naxos) entitled to designate a director pursuant to Section 3.2 above may also be an Affiliate of an entity that is engaged in the business of investing and reinvesting in other entities (each such entity, a “Fund”). As such, the Fund, and by extension the Investor and any director designated by such Investor, may acquire knowledge of competitors, potential transactions or other matters which may present both a corporate opportunity for the Corporation and an investment opportunity for such Fund (“Corporate Opportunity”). In such circumstances, the director-designee shall not be required to disclose such Corporate Opportunity to the Board and, to the fullest extent permitted by law, shall have fully satisfied and fulfilled such director’s fiduciary duty to the Corporation and its Security Holders with respect to such Corporate Opportunity, and the Corporation, to the fullest extent permitted by law, waives any claim that such Corporate Opportunity constituted an opportunity that should have been presented to the Corporation or any of its Affiliates, if such director acts in good faith in a manner consistent with the following policy: “A Corporate Opportunity offered to any person who is a director of the Corporation, and who is also a partner or employee of a Fund shall belong to such Fund, unless such opportunity was expressly offered to such person solely in his or her capacity as a director of the Corporation.” Notwithstanding the foregoing, absent the express written consent of the applicable Investor, no other Conflict of Interest Policy or other policy enacted by Corporation or the Board, including but not limited to the that certain Directors Code of Conduct and Conflict of Interest Policy, shall be binding on such Investor’s designated-director.

Notwithstanding the preceding, but, for so long as the Corporation has not completed an initial public offering of its Shares, subject to the Corporate Opportunity rights (including the right not to disclose a Corporate Opportunity to the Board) granted above to any director designated by an Investor that is a Fund or an Affiliate of a Fund (i) all directors of the Corporation must, at all times, disclose a potential, real or perceived conflict of interest in regards to any board discussions or proposed resolution as soon as the issue arises, except that a director-designee of a Fund shall never be deemed to be in a potential, real or perceived conflict

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of interest in respect of a Corporate Opportunity and (ii) in such event or in the event the majority of the Board substantiate that a director is in a position of conflict of interest in regards to any board discussion or proposed resolution, such director shall recuse itself from any such board discussion or proposed resolution, upon notice from the Board.

3.7 Electronic Participation. Any meeting of the Board may be held by telephone, videoconference or any other means of telecommunication. To the extent that the Naxos Nominee or the Sofinnova Nominee or the Mitsui Nominee or the Lanxess Nominee or any Observer (as defined below) is unable to attend any meetings of the Board in person, the Corporation agrees to allow any such nominee that is unable to attend in person to participate to such meetings via telephone conference call, videoconference, or some combination of the foregoing.

Notwithstanding the foregoing, the consent of the Investors shall not be required in order for the Corporation to enter into and perform its obligations under (a) the Heads of Agreement with Lanxess Corporation and (b) the agreements contemplated by the Heads of Agreement in such forms as may be approved by any officer of the Corporation as conclusively evidenced by any such officer’s execution and delivery thereof. “Heads of Agreement” shall have the meaning given to such term in the Stock Purchase Agreement dated February 6^th, 2012 between the Corporation and Lanxess Corporation.

The Corporation and the Board shall at all times cause to be maintained a Strategic Opportunities Committee (the “Strategic Opportunities Committee”), which shall be comprised of the Chairman of the Audit Committee, the CEO of the Company and a representative of each of the Investors holding more than fifteen percent (15%) of the total number of Shares then outstanding, such representative being either a Director or an Observer nominated by such Investor. The Strategic Opportunities Committee may invite any other Director or Observer to attend its meetings as an observer. The Strategic Opportunities Committee’s duties shall be as set forth in the enabling charter approved by the Board, and essentially consist of (i) screening the Corporation’s strategic opportunities, (ii) considering which such opportunities are to be referred to the Board and (iii) reporting and recommending to the Board in respect

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of such opportunities. The Strategic Opportunities Committeeshall meet at least four (4) times annually, or more frequently as circumstances dictate.Any meeting of the Strategic Opportunities Committee may be held by telephone, videoconference or any other means of telecommunication.

“THE SECURITIES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO AN AMENDED AND RESTATED SHAREHOLDERS’ AGREEMENT DATED AS OF APRIL 15, 2011 (AS AMENDED BY THAT CERTAIN FIRST AMENDMENT, DATED AS OF NOVEMBER 4, 2011 AND AS AMENDED BY THAT CERTAIN SECOND AMENDMENT, DATED AS OF FEBRUARY 6, 2012, THE “SHAREHOLDERS’ AGREEMENT”) BY AND AMONG BIOAMBER INC. (THE “CORPORATION”) AND CERTAIN OF THE CORPORATION’S SHAREHOLDERS. THE TERMS OF SUCH SHAREHOLDERS’ AGREEMENT INCLUDE, AMONG OTHER THINGS, A VOTING AGREEMENT AMONG CERTAIN OF THE CORPORATION’S SHAREHOLDERS AND CONTRACTUAL PREEMPTIVE RIGHTS, IN FAVOR OF THE HOLDER HEREOF AND THE OTHER HOLDERS OF SHARES (AS SUCH TERM IS DEFINED THEREIN), ON CERTAIN ISSUANCES BY THE CORPORATION. A COPY OF SUCH SHAREHOLDERS’ AGREEMENT WILL BE FURNISHED WITHOUT CHARGE BY THE CORPORATION TO THE HOLDER HEREOF UPON WRITTEN REQUEST.”

and (iv) LanxessCorporation hereunder to designate and/or remove the Lanxess Nominee, any other approval or consent rights of LanxessCorporation or the Lanxess Nominee, or any other right or obligations of LanxessCorporation under this Agreement, may not be amended, modified or waived (for so long as Lanxess is entitled to designate the Lanxess Nominee pursuant to the terms of this Agreement) without the consent of LanxessCorporation.

Lanxess Corporation

111 RIDC Park West Drive

Pittsburgh

Pennsylvania ###-###-####

Attention: Marcy Tenaglia, Vice President, General Counsel and Secretary

Facsimile: ***

E-mail: ***

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(signatures on next pages)

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IN WITNESS WHEREOF the parties have signed this Amendment at the place and as of the date first mentioned above.

[Signature Page – Second Amendment dated February 6, 2012 to the Amended and Restated shareholders agreement

of BioAmber Inc.]

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[Signature Page – Second Amendment dated February 6, 2012 to the Amended and Restated shareholders agreement

of BioAmber Inc.]

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