UNITED STATES SECURITIES AND EXCHANGE
COMMISSION



Washington, D.C. 20549



Amendment No. 1

to

Form 10-K



|                                            | þANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934    
|------------------------------------------- | -----------------------------------------------------------------------------------------
|                                            |                                                                                          
|For the fiscal year ended December 31, 2012
|                                            |                                                                                          
|or                                         
|                                            |                                                                                          
|                                            | oTRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934



Commission file number 001-35138



PIMI AGRO CLEANTECH, INC.

(Exact name of registrant as specified
in its charter)



|Delaware                        | 26-4684680         
|------------------------------- | -------------------
|(State or other jurisdiction of | (I.R.S. Employer   
|Incorporation or organization)  | Identification No.)



269 South Beverly Drive Suite 1091

Beverly Hills California 90212 USA

(Address of
principal executive offices)



(310) 203-8278

( Registrant’s telephone
number, including area code )



Securities registered pursuant to Section
12(b) of the Act: None



Securities registered pursuant to Section
12(g) of the Act: Common Stock, $.01 Par Value Per Share



Indicate by check mark whether the registrant
is a well-known seasoned issuer as defined in Rule 405 of the Securities Act.

Yes  ̈ No x



Indicate by check mark if the registrant
is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.

Yes  ̈  No x



Indicate by check mark whether the registrant
(1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding
12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes x No  ̈



Indicate by check mark if disclosure of
delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s
knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment
to this Form 10-K. x



Indicate by check mark whether the registrant
is a large accelerated filer, an accelerated filer, or a non-accelerated filer. See definition of “accelerated filer and
large accelerated filer” in Rule 12b-2 of the Exchange Act. (Check one):



Large accelerated filer
o  Accelerated filer o Non-accelerated
filer o Smaller reporting company x





As of January 31, 2013, the aggregate market
value of the issued and outstanding common stock held by non-affiliates of the registrant, computed by reference to the price at
which the common equity was last sold of $0.80 was approximately $2,640,917. For purposes of the above statement only, all directors,
executive officers and 10% shareholders are assumed to be affiliates. This determination of affiliate status is not necessarily
a conclusive determination for any other purpose.



Number of shares of common stock outstanding
as of March 12, 2013 was 9,336,487.





1









CAUTIONARY NOTE
REGARDING FORWARD-LOOKING STATEMENTS



In this annual report, references to "Pimi
Agro Cleantech, Inc.," "Pimi," "the Company," "we," "us," and "our" refer
to Pimi Agro Cleantech, Inc. and its subsidiary, Pimi Agro CleanTech, Ltd.



Except for the historical information contained
herein, some of the statements in this Report contain forward-looking statements that involve risks and uncertainties. These statements
are found in the sections entitled "Business," "Management's Discussion and Analysis of Financial Condition and
Results of Operation," and "Risk Factors." They include statements concerning: our business strategy; expectations
of market and customer response; liquidity and capital expenditures; future sources of revenues; expansion of our proposed product
line; and trends in industry activity generally. In some cases, you can identify forward-looking statements by words such as "may,"
"will," "should," "expect," "plan," "could," "anticipate," "intend,"
"believe," "estimate," "predict," "potential," "goal," or "continue"
or similar terminology. These statements are only predictions and involve known and unknown risks, uncertainties and other factors,
including, but not limited to, the risks outlined under "Risk Factors," that may cause our or our industry's actual results,
levels of activity, performance or achievements to be materially different from any future results, levels of activity, performance
or achievements expressed or implied by such forward-looking statements. For example, assumptions that could cause actual results
to vary materially from future results include, but are not limited to: our ability to successfully develop and market our products
to customers; our ability to generate customer demand for our products in our target markets; the development of our target markets
and market opportunities; our ability to manufacture suitable products at competitive cost; market pricing for our products and
for competing products; the extent of increasing competition; technological developments in our target markets and the development
of alternate, competing technologies in them; and sales of shares by existing shareholders. Although we believe that the expectations
reflected in the forward looking statements are reasonable, we cannot guarantee future results, levels of activity, performance
or achievements. Unless we are required to do so under federal securities laws or other applicable laws, we do not intend to update
or revise any forward-looking statements.





Documents Incorporated by Reference:Not Applicable





Explanatory Note



The purpose of this Amendment No. 1 to
Pimi Agro Cleantech, Inc.’s Annual Report on Form 10-K for the fiscal year ended December 31, 2012 (the “Form 10-K”),
as filed with the Securities and Exchange Commission on March 25, 2013, is to furnish Exhibit 10.43 to the Form 10-K. This Amendment
No. 1 to the Form 10-K updates the Exhibit Index to reflect the furnishing of Exhibits 10.43.



No other changes have been made to the
Form 10-K.  This Amendment No. 1 to the Form 10-K continues to speak as of the original filing date of the Form 10-K,
does not reflect events that may have occurred subsequent to the original filing date, and does not modify or update in any way
the disclosures made in the original Form 10-K.







2







ITEM 15. EXHIBITS AND FINANCIAL STATEMENT
SCHEDULES





|Exhibit 
Number |  | Description                                                                                                                                                                                                                                                                                                                   
|--------------- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|3.1             |  | Articles of Incorporation of Pimi Agro Cleantech Ltd. (incorporated by reference to the Company’s registration on Form S-1 filed with the Securities and Exchange Commission on May 5, 2009)                                                                                                                                  
|                |  |                                                                                                                                                                                                                                                                                                                               
|3.2             |  | Change of Name Certificate of Pimi Agro Cleantech Ltd. (incorporated by reference to the Company’s registration on Form S-1 filed with the Securities and Exchange Commission on May 5, 2009)                                                                                                                                 
|                |  |                                                                                                                                                                                                                                                                                                                               
|3.3             |  | Certificate of Incorporation of Pimi Agro Cleantech, Inc. (incorporated by reference to the Company’s registration on Form S-1 filed with the Securities and Exchange Commission on May 5, 2009)                                                                                                                              
|                |  |                                                                                                                                                                                                                                                                                                                               
|3.4             |  | By-laws of Pimi Agro Cleantech Ltd. (incorporated by reference to the Company’s registration on Form S-1 filed with the Securities and Exchange Commission on May 5, 2009)                                                                                                                                                    
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.1            |  | Employment Agreement by and between Mr. Youval Saly and Pimi Agro Cleantech Ltd. dated November 27, 2006. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                           
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.2            |  | Addendum to the Employment Agreement with Mr. Youval Saly dated October 29, 2008. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                                   
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.3            |  | Employment Agreement with Mr. Nimrod Ben Yehuda dated November 13, 2005. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                                            
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.4            |  | Addendum to the Employment Agreement with Mr. Nimrod Ben Yehuda dated November 15, 2006 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                             
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.5            |  | Addendum to the Employment agreement with Mr. Nimrod Ben Yehuda dated April 28, 2009 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                                
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.6            |  | Employment Agreement by and between Mr. Ami Sivan and Pimi Agro Cleantech Ltd. dated May 15, 2012 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on May 30, 2012)                                                                                                     
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.7            |  | Reserved                                                                                                                                                                                                                                                                                                                      
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.8            |  | Employment Agreement by and between Mr. Avi Lifshitz and Pimi Agro Cleantech Ltd. dated November 19, 2008 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                           
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.9            |  | Pimi Agro Cleantech Ltd. 2008 Share Option Plan and option Agreements with: Mr. Youval Saly, Mr. Avi Lifshitz, Mr. Avi Levi, Mr. Doron Shorrer, Prof. Avi Nachmias, Prof. Ilan Chet. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.10           |  | Agreement between Machteshim Chemical Works Ltd. and Nir Ecology Ltd. dated July 12, 2004. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                          
|                |  |                                                                                                                                                                                                                                                                                                                               
|10.11           |  | Agreement between Nir Ecology Ltd. and Pimi Agro Cleantech Ltd both dated November 11, 2005 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                         





3







|      |  |                                                                                                                                                                                                                                                                                                                
|----- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|10.12 |  | Agreement between Nir Ecology Ltd. and Pimi Agro Cleantech Ltd both dated November 11, 2005 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                          
|      |  |                                                                                                                                                                                                                                                                                                                
|10.13 |  | Investment Agreement between Mr. Ben Yehuda, Omdan Consulting and Instruction Ltd., Mr. Carmel and JNS Capital LLC dated November 13, 2005. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on August 3, 2009)                        
|      |  |                                                                                                                                                                                                                                                                                                                
|10.14 |  | Addendum to the Investment Agreement between Mr. Ben Yehuda, Omdan Consulting and Instruction Ltd., Mr. Carmel and JNS Capital LLC dated November 15, 2006 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)           
|      |  |                                                                                                                                                                                                                                                                                                                
|10.15 |  | Overseas Market Development Consultancy Agreement by and between Pimi Agro Cleantech Ltd. and The Center for Potato Research in a Warm Climate dated January 9, 2008. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)
|      |  |                                                                                                                                                                                                                                                                                                                
|10.16 |  | MOU between Pimi Agro Cleantech LTD. and Omnivent Techniek BV dated May 19, 2008. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                    
|      |  |                                                                                                                                                                                                                                                                                                                
|10.17 |  | Agreement for Services by and between Wagner Regulatory Associates, Inc. Pimi Agro Cleantech Ltd. dated September 21, 2008 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                           
|      |  |                                                                                                                                                                                                                                                                                                                
|10.18 |  | Tenancy Agreement between Kibbutz Alonim and Pimi Agro Cleantech Ltd dated December 30, 2008. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                        
|      |  |                                                                                                                                                                                                                                                                                                                
|10.19 |  | Agreement between Redebel S.A. and Pimi Cleantech Ltd. (Registration Assistance Agreement) dated December 23, 2008. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                  
|      |  |                                                                                                                                                                                                                                                                                                                
|10.20 |  | Agreement by and between Omex Agriculture Ltd. and Pimi Agro Cleantech Ltd. dated January 11, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)*                                                                 
|      |  |                                                                                                                                                                                                                                                                                                                
|10.21 |  | Letter of Intent Agreement by and between VegiSafe LLC and Pimi Agro Cleantech Ltd. dated January 20, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on August 3, 2009)                                                        
|      |  |                                                                                                                                                                                                                                                                                                                
|10.22 |  | Term Sheet with Earthbound LLC dated January 20, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                                               
|      |  |                                                                                                                                                                                                                                                                                                                
|10.23 |  | Voting Agreement between Alon Carmel, Omdan Consulting, and Instruction Ltd and Nir Ecology dated February 24, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                 
|      |  |                                                                                                                                                                                                                                                                                                                
|10.24 |  | Addendum to the Voting Agreement of February 24, 2009 dated April 23, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                          





4







|      |  |                                                                                                                                                                                                                                                                                                      
|----- |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|10.25 |  | Share Exchange Agreement between Pimi Agro Cleantech Inc., Pimi Agro Cleantech Ltd. and the Shareholders of Pimi Agro Cleantech Ltd., dated April 27, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)
|      |  |                                                                                                                                                                                                                                                                                                      
|10.26 |  | Pimi Agro Cleantech, Inc. 2009 Stock Incentive Plan. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                                                       
|      |  |                                                                                                                                                                                                                                                                                                      
|10.27 |  | Warrant issued by Pimi Agro Cleantech, Inc. to Earthbound LLC dated May 3, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                                           
|      |  |                                                                                                                                                                                                                                                                                                      
|10.28 |  | Amendment to Warrant issued by Pimi Agro Cleantech, Inc. to Earthbound LLC dated June 7, 2009. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                             
|      |  |                                                                                                                                                                                                                                                                                                      
|10.29 |  | Amendment to Warrant issued by Pimi Agro Cleantech, Inc. to Earthbound LLC dated July 29, 2009 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on August 3, 2009).                                                          
|      | 
|10.30 |  | Stock Purchase Agreement by and between Pimi Agro Cleantech, Inc. and Ehud Nahum dated June 4, 2009 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                        
|      |  |                                                                                                                                                                                                                                                                                                      
|10.31 |  | Stock Purchase Agreement by and between Pimi Agro Cleantech, Inc. and Yuval Nahum dated June 4, 2009 (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)                                                       
|      |  |                                                                                                                                                                                                                                                                                                      
|10.32 |  | Financial Advisory Agreement by and between Pimi Agro Cleantech, Inc. and Lampost Capital L.C., dated March 24, 2010 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on March 29, 2010)                                                       
|      |  |                                                                                                                                                                                                                                                                                                      
|10.33 |  | Subscription Agreement by and between Pimi Agro Cleantech, Inc. and the subscribers thereto, dated April 15, 2010 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on April 21, 2010)                                                          
|      |  |                                                                                                                                                                                                                                                                                                      
|10.34 |  | Stock Purchase Agreement dated August 24, 2010 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on August 30, 2010).                                                                                                                           
|      |  |                                                                                                                                                                                                                                                                                                      
|10.35 |  | Warrant dated August 24, 2010 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on August 30, 2010).                                                                                                                                            
|      |  |                                                                                                                                                                                                                                                                                                      
|10.36 |  | Agreement dated December 28, 2010 by and
        between Pimi Agro Cleantech, Inc. and Mr. Uri Sheinbaum (incorporated by reference to the Company’s Form 8-K filed with the
        Securities and Exchange Commission on January 4, 2011).                                                         
|      |  |                                                                                                                                                                                                                                                                                                      
|10.37 |  | Subscription Agreement dated December 28,
        2010 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on January 4,
        2011).                                                                                                           





5







|      |  |                                                                                                                                                                                                                                           
|----- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|10.38 |  | Warrant dated December 28, 2010 (incorporated
        by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on January 4, 2011).                                                                       
|      |  |                                                                                                                                                                                                                                           
|10.39 |  | Securities Purchase Agreement dated January
        25, 2011 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on January
        31, 2011).                                         
|      |  |                                                                                                                                                                                                                                           
|10.40 |  | Warrant dated January 25, 2011 (incorporated
        by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on January 31, 2011).                                                                       
|      |  |                                                                                                                                                                                                                                           
|10.41 |  | Addendum No 1 to Letter of Intent dated January 20, 2009, between Pimi Agro Cleantech Inc, and Vegisafe LLC. (incorporated by reference to the Company’s Form 10-K filed with the Securities and Exchange Commission on April 12, 2011)   
|      |  |                                                                                                                                                                                                                                           
|10.42 |  | Subscription Agreement by and between Pimi Agro Cleantech, Inc. and the subscribers thereto, dated March 9, 2012 (incorporated by reference to the Company’s Form 8-K filed with the Securities and Exchange Commission on March 12, 2012)
|      |  |                                                                                                                                                                                                                                           
|10.43 |  | Addendum to Agreement dated December 28, 2010 by and between Pimi Agro Cleantech, Inc. and Mr. Uri Sheinbaum (item 10.36) (filed herewith)                                                                                                
|      |  |                                                                                                                                                                                                                                           
|21.1  |  | List of subsidiaries of the Company. (incorporated by reference to the Company’s registration on Form S-1 filed with the Securities and Exchange Commission on May 5, 2009)                                                               
|      |  |                                                                                                                                                                                                                                           
|31.1  |  | Certification by Chief Executive Officer pursuant to Sarbanes Oxley Section 302 (filed herewith).                                                                                                                                         
|      |  |                                                                                                                                                                                                                                           
|31.2  |  | Certification by Chief Financial Officer pursuant to Sarbanes Oxley Section 302 (filed herewith).                                                                                                                                         



|32.1 |  | Certification by Chief Executive Officer pursuant to 18 U.S.C. Section 1350 (filed herewith).
|---- |  | ---------------------------------------------------------------------------------------------



|32.2 |  | Certification by Chief Financial Officer pursuant to 18 U.S.C. Section 1350 (filed herewith).
|---- |  | ---------------------------------------------------------------------------------------------



|99.2 |  | Approval of Office of the Chief Scientist, Ministry of Industry, Trade and Labor, State of Israel, dated April 11, 2007. (incorporated by reference to the Company’s registration on Form S-1/A filed with the Securities and Exchange Commission on July 2, 2009)
|---- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



|99.2 |  | Approval of Office of the Chief Scientist, Ministry of Industry, Trade and Labor, State of Israel, dated November 12, 2007. (incorporated by reference to the Company’s registration on Form S-1 filed with the Securities and Exchange Commission on May 5, 2009)
|---- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|     |  |                                                                                                                                                                                                                                                                   

*Portions of exhibit
10.20 have been omitted pursuant to a request for confidential treatment filed separately with the Securities and Exchange Commission.





6







SIGNATURES



Pursuant to the requirements of Section 13
or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned,
thereunto duly authorized.



|              | PIMI AGRO CLEANTECH, INC. |                                             
|------------- | ------------------------- | --------------------------------------------
|              |                           |                                             
|April 7, 2013 | By:                       | /s/ Ami Sivan                               
|              |                           | Ami Sivan                                   
|              |                           | Chief Executive Officer                     
|              |                           | (Principal Executive Officer)               
|              |                           |                                             
|April 7, 2013 | By:                       | /s/ Avi Lifshitz                            
|              |                           | Avi Lifshitz                                
|              |                           | Chief Financial Officer                     
|              |                           | (Principal Financial and Accounting Officer)



Pursuant to the requirements of the Securities
Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities
and on the dates indicated.



|Signature             |  | Title                                                          |  | Date         
|--------------------- |  | -------------------------------------------------------------- |  | -------------
|                      |  |                                                                |  |              
|                      |  |                                                                |  |              
|/s/ Ami Sivan         |  | Chief Executive Officer                                        |  | April 7, 2013
|Ami Sivan             |  | (Principal Executive Officer)                                  |  |              
|                      |  |                                                                |  |              
|/s/ Avi Lifshitz      |  | Chief Financial Officer                                        |  | April 7, 2013
|Avi Lifshitz          |  | (Principal Financial Officer and Principal Accounting Officer) |  |              
|                      |  |                                                                |  |              
|/s/ Alon Carmel       |  | Chairman of the Board                                          |  | April 7, 2013
|Alon Carmel           |  |                                                                |  |              
|                      |  |                                                                |  |              
|/s/ Nimrod Ben-Yehuda |  | Chief Technology Officer, Director                             |  | April 7, 2013
|Nimrod Ben-Yehuda     |  |                                                                |  |              
|                      |  |                                                                |  |              
|/s/ Doron Shorrer     |  | Director                                                       |  | April 7, 2013
|Doron Shorrer         |  |                                                                |  |              







7