Exhibit 10.39

THIRD AMENDMENT OF AMENDED AND RESTATED VENTURE LOAN AND SECURITY AGREEMENT

This THIRD AMENDMENT OF AMENDED AND RESTATED VENTURE LOAN AND SECURITY AGREEMENT (this “Agreement”), dated as of June 29, 2012, is entered into by and among ENPHASE ENERGY, INC., a Delaware corporation (“Borrower”), HORIZON TECHNOLOGY FINANCE CORPORATION (“Horizon”), a Delaware corporation and HORIZON CREDIT I LLC (“HCI” and collectively with Horizon, “Lender”), a Delaware limited liability company, as assignee and holder of Advance (Loan A).

RECITALS

A. Pursuant to that certain Amended and Restated Venture Loan and Security Agreement dated as of March 25, 2011, as amended on June 30, 2011 and December 30, 2011 (as the same has been and may be further amended, supplemented or otherwise modified from time to time, the “Loan Agreement”) between Borrower and Lender, Lender, among other things, has (i) provided certain loans to Borrower as evidenced by (a) a certain Secured Promissory Note (Loan A) executed by Borrower in favor of Lender, dated as of March 11, 2010, in the original principal amount of Seven Million Dollars ($7,000,000.00) (“Note A”), (b) a certain Secured Promissory Note (Loan B) executed by Borrower in favor of Lender, dated as of March 25, 2011, in the original principal amount of Two Million Dollars ($2,000,000.00) (“Note B”) and (c) a certain Secured Promissory Note (Loan C) executed by Borrower in favor of Lender, dated as of September 23, 2011, in the original principal amount of Three Million Dollars ($3,000,000) (“Note C” and together with Note A and Note B, the “Notes”) and (ii) been granted a security interest in all assets of Borrower, except for Borrower’s Intellectual Property (as defined in the Loan Agreement) and certain specified equipment.

B. Borrower has now requested that Lender amend the restrictions on maintenance of bank accounts within the negative covenants of the Loan Agreement.

C. Lender is willing to grant such request, but only to the extent, and in accordance with the terms, and subject to the conditions, set forth herein.

AGREEMENT

NOW, THEREFORE, in consideration of the above recitals and for other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, Borrower and Lender hereby agree as follows:

“7.13 Maintenance of Accounts. (i) Maintain any deposit account or account holding securities owned by Borrower except (a) accounts with the lender providing Borrower with Indebtedness permitted under subsection (d) of the definition of Permitted Indebtedness or (b) accounts with respect to which Lender is able to take such actions as it deems necessary to obtain a perfected security interest in such accounts through one or more Account Control Agreements; or (ii) grant or allow any other Person (other than Lender) to perfect a security interest in, or enter into any agreements with any Persons (other than Lender) accomplishing perfection via control as to any of its deposit accounts or accounts holding securities other than in favor of the lender providing Borrower with Indebtedness permitted under subsection (d) of the definition of Permitted Indebtedness. Notwithstanding the foregoing: (1) Borrower may maintain deposit accounts containing up to twenty percent (20%) of its unrestricted cash in accounts held outside of the United States, and (2) Borrower may maintain a deposit account with Bank of the West, having an account number of 023496125 (the “Bank of the West Account”), provided that not more than Five Thousand Dollars ($5,000) is maintained by the Borrower in the Bank of the West Account.”

(a) Borrower executing and delivering an executed copy of this Agreement; and

(b) Borrower’s agreement to pay, when invoiced, Lender’s in-house legal expenses in the amount of One Thousand Five Hundred and 00/100 Dollars ($1,500.00) incurred in connection with the drafting, negotiation and execution of this Agreement.

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IN WITNESS WHEREOF, Borrower and Lender have caused this Agreement to be executed as of the day and year first above written.

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