UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 3)*

SOLAZYME, INC.

(Name of Issuer)

COMMON STOCK, PAR VALUE $0.001 PER SHARE

(Title of Class of Securities)

83415T 101

(CUSIP Number)

Daniel H. Miller

The Roda Group

918 Parker Street

Berkeley, California 94710

(510) 649-1900

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

August 14, 2013

(Date of Event, which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box  ¨.

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See § 240.13d-7 for other parties to whom copies are to be sent.

The Information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

Explanatory Note

This Amendment No. 3 to Schedule 13D (this “Amendment No. 3”) amends the statement on Schedule 13D which was originally filed by the Reporting Persons with the Securities and Exchange Commission (the “Commission”) on February 14, 2012, as amended by Amendment No. 1 to the Schedule 13D as filed with the Commission on February 25, 2013, as amended by Amendment No. 2 to the Schedule 13D as filed with the Commission on June 7, 2013 (collectively, the “Statement”), with respect to the Common Stock, par value $0.001 per share (the “Shares”), of Solazyme, Inc. This Amendment No. 3 amends the Statement as specifically set forth herein. Unless otherwise indicated herein, each capitalized term used but not otherwise defined herein shall have the meaning assigned to such term in the Statement.

Item 5. Interest in Securities of the Issuer.

Item 5 shall be amended and restated in its entirety:

(a) As of the date hereof, (i) Roda XIV directly owns 1,341,225 Shares, representing approximately 2.15% of the Shares outstanding, (ii) Roda XV owns 24,812 Shares, representing approximately 0.04% of the Shares outstanding, (iii) Roda XVII owns 302,342 Shares, representing approximately 0.49% of the Shares outstanding, (iv) Roda XVIII owns 607,335 Shares, representing approximately 0.97% of Shares outstanding, (v) Roda XIX owns 290,924 Shares, representing approximately 0.47% of the Shares outstanding, (vi) Roda XX owns 151,615 Shares, representing approximately 0.24% of the Shares outstanding, and (vii) Roda VDC owns 20,842 Shares, representing approximately 0.03% of the Shares outstanding (collectively, the “Roda Shares”).

Daniel H. Miller, in his capacity as managing member, may be deemed to have indirect beneficial ownership of the Roda Shares. In addition, Mr. Miller has direct beneficial ownership of 1,764,386 Shares, representing 2.83% of the Shares outstanding, held by the Daniel H. Miller Revocable Trust. Mr. Miller directly owns 25,000 Shares, representing 0.04% of the Shares outstanding. Mr. Miller also may be deemed to have indirect beneficial ownership of 60,285 Shares, representing 0.10% of the Shares outstanding, held by The Strauch 1994 Grandchildren’s Trust II. In addition, Mr. Miller may be deemed to have indirect beneficial ownership of 45,000 Shares, representing 0.07% of the Shares outstanding, held by Carolyn C. Miller; such shares were transferred to Ms. Miller from the Daniel H. Miller Revocable Trust as part of ongoing divorce proceedings.

Roger Strauch, in his capacity as managing member, may be deemed to have indirect beneficial ownership of the Roda Shares. In addition, Mr. Strauch has direct beneficial ownership of 1,719,391 Shares, representing 2.76% of the Shares outstanding, held by the The Strauch Kulhanjian Family Trust. Mr. Stauch directly owns 348,775 Shares, representing 0.56% of the Shares outstanding. Mr. Strauch may also be deemed to have indirect beneficial ownership of (i) 318,229 Shares, representing 0.51% of the Shares outstanding, held by The Strauch Kulhanjian 2007 Irrevocable Children’s Trust, (ii) 91,228 Shares, representing 0.15% of the Shares outstanding, held by The DCM Educational Trust, (iii) 77,404 Shares, representing 0.12% of the Shares outstanding, held by The Emmeline Maeve McPherson Miller Trust, (iv) 77,404 Shares, representing 0.12% of the Shares outstanding, held by The Cooper Odgen Miller Trust, (v) 60,000 Shares, representing 0.10% of the Shares outstanding, held by The Paul Kulhanjian Strauch 2007 Irrevocable Trust, (vi) 60,000 Shares, representing 0.10% of the Shares outstanding, held by The Nairi Susan Kulhanjian Strauch 2007 Irrevocable Trust, and (vii) 60,000 Shares, representing 0.10% of the Shares outstanding, held by The Alexan Kulhanjian Strauch 2007 Irrevocable Trust.

(b) With respect to the Shares reported herein, each of Roda XIV, Roda XV, Roda XVII, Roda XVIII, Roda XIX, Roda XX and Roda VDC may be deemed to have sole voting and dispositive power to direct the vote and disposition of the Shares, which such Reporting Person may be deemed to beneficially own as set forth above.

With respect to the Shares reported herein, Daniel H. Miller may be deemed to have shared voting and dispositive power to direct the vote and disposition of the Roda Shares. Mr. Miller may be deemed to have sole voting and dispositive power to direct the vote and disposition of the Shares, which Mr. Miller may be deemed to have indirect beneficial ownership as set forth above. Mr. Miller has sole voting and dispositive power to direct the vote and disposition of the Shares that Mr. Miller holds directly.

With respect to the Shares reported herein, Roger A. Strauch may be deemed to have shared voting and dispositive power to direct the vote and disposition of the Roda Shares. Mr. Strauch may be deemed to have sole voting and dispositive power to direct the vote and disposition of the Shares, which Mr. Strauch may be deemed to have indirect beneficial ownership as set forth above. Mr. Strauch has sole voting and dispositive power to direct the vote and disposition of the Shares that Mr. Strauch holds directly.

Neither the filing of this Statement nor any of its contents shall be deemed to constitute an admission by any of the Reporting Persons that it is the beneficial owner of any of the Share referred to herein for the purposes of Section 13(d) of the Securities Exchange Act of 1934, or for any other purpose, and such beneficial ownership is expressly disclaimed by each Reporting Person.

(c) On June 28, 2013, The Daniel H. Miller Revocable Trust transferred 100,000 Shares to Carolyn C. Miller as part of ongoing divorce proceedings.

On July 12, 2013, Carolyn C. Miller sold 10,000 Shares for a weighted average price of $10.9198 per Share in an open market transaction.

On July 19, 2013, Carolyn C. Miller sold 10,000 Shares for a weighted average price of $11.6777 per Share in an open market transaction.

On July 26, 2013, Carolyn C. Miller sold 10,000 Shares for a weighted average price of $11.6984 per Share in an open market transaction.

On August 2, 2013, Carolyn C. Miller sold 5,000 Shares for a weighted average price of $11.1700 per Share in an open market transaction.

On August 5, 2013, Carolyn C. Miller sold 5,000 Shares for a weighted average price of $11.2834 per Share in an open market transaction.

On August 8, 2013, The Daniel H. Miller Revocable Trust sold 25,000 Shares for a weighted average price of $11.9667 per Share in an open market transaction.

On August 9, 2013, The Daniel H. Miller Revocable Trust sold 25,000 Shares for a weighted average price of $12.7547 per Share in an open market transaction.

On August 13, 2013, Carolyn C. Miller sold 10,000 Shares for a weighted average price of $11.9777 per Share in an open market transaction.

On August 14, 2013, Carolyn C. Miller sold 5,000 Shares for a weighted average price of $12.7887 per Share in an open market transaction.

(d) Not applicable.

(e) Not applicable.

2

SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Dated: August 21, 2013