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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

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FORM 10-K/A
Amendment No. 1

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|x                                                        | ANNUAL   REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934    
|-------------------------------------------------------- | ------------------------------------------------------------------------------------------
|                                                         | For the fiscal year ended: September 30, 2006                                             
|                                                         |                                                                                           
|OR                                                      
|                                                         |                                                                                           
|o                                                        | TRANSITION   REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|                                                         | For   the transition period from __________ to __________                                 
|                                                         |                                                                                           
|Commission File Number: 0-11412                         
|                                                         |                                                                                           
|AMTECH   SYSTEMS, INC.                                  
|(Exact   name of registrant as specified in its charter)

|Arizona                                                            |  | 86-0411215                              
|------------------------------------------------------------------ |  | ----------------------------------------
|                                                                   |  |                                         
|(State or   other jurisdiction of   incorporation or organization) |  | (I.R.S.   Employer   Identification No.)
|                                                                   |  |                                         
|131 South Clark Drive, Tempe, Arizona                              |  | 85281                                   
|                                                                   |  |                                         
|(Address   of principal executive offices)                         |  | (Zip Code)                              

Registrants telephone number, including area code: 480-967-5146 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 (Title of Class)

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 | o | 
| | --- | - |  | -- | - | 

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.
o

Indicate by check mark whether the registrant is an accelerated filer (as defined in Exchange Act Rule 12(b)(2).

| | Yes | o |  | No | x | 
| | --- | - |  | -- | - | 
| |     |   |  |    |   | 

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EXPLANATORY NOTE

This is Amendment No. 1 to the Registrants annual report on Form 10-K for the year ended September 30, 2006, which was originally filed with the Securities and Exchange Commission on December 21, 2006. This amendment is being filed to include the Registrants response to Item 14 required by Part III, which originally was expected to be incorporated by reference to the Registrants definitive Proxy Statement to be delivered to its shareholders in connection with its 2007 Annual Meeting of Shareholders.  Responses to Items 10,11,12 and 13 of Part III were included in the Registrants Annual Report on Form 10-K for the year ended September 30, 2006, which was originally filed with the Securities and Exchange Commission on December 21, 2006.

TABLE OF CONTENTS

|           |                                              |  | Page
|---------- | -------------------------------------------- |  | ----
|           |                                              |  |     
|           | PART III                                     |  |     
|Item   14. | Principal   Accountant Fees and Services     |  | 2   
|           | PART IV.                                     |  |     
|Item 15.   | Exhibits and   Financial Statement Schedules |  | 4   
|Signatures |                                              |  | 5   

PART III

|ITEM 14. | PRINCIPAL   ACCOUNTING FEES AND SERVICES
|-------- | ----------------------------------------

The following table sets forth the fees billed to us by our independent auditors during the years ended September 30, 2006 and 2005 for: (i) services rendered for the audit of our annual financial statements and the review of our quarterly financial statements, (ii) services by our auditor that are reasonably related to the performance of the audit or review of our financial statements and that are not reported as audit fees, (iii) services rendered in connection with tax compliance, tax advice and tax planning, and (iv) all other fees for services rendered.

|                       |  | Year Ended   Sept. 30, 2006 |         | Year Ended   Sept. 30, 2005 |  
|---------------------- |  | --------------------------- | ------- | --------------------------- | -
|                       |  |                             |         |                             |  
|Audit Fees             |  | $                           | 187,500 |                             | $
|Audit-Related Fees (1) |  |                             |        |                             |  
|Tax Fees               |  |                             |        |                             |  
|All Other Fees         |  |                             |        |                             |  
|                       |  |                             |         |                             |  
|Total Fees             |  | $                           | 187,500 |                             | $
|                       |  |                             |         |                             |  

|   
|---
|(1)

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PRE-APPROVAL POLICY

In May 2003, the Audit Committee adopted a Pre-Approval Policy (the Policy) governing the approval of all audit and non-audit services performed by the Companys independent auditor in order to ensure that the performance of such services does not impair the auditors independence.

According to the Policy, the Audit Committee will annually review and pre-approve the types of services, and will set a limit on the fees for such services, that may be provided by the independent auditor during the following year. The Policy specifically describes the annual audit services and fees, other services that are audit-related, the preparation of tax returns and tax related compliance services and all other services that have the general pre-approval of the Audit Committee. The term of any general pre-approval is twelve (12) months from the date of pre-approval, unless the Audit Committee specifically provides for a different period.

Any service to be provided by the independent auditor that has not received general pre-approval under the Policy is required to be submitted to the Audit Committee for approval prior to the commencement of a substantial portion of the engagement. Any proposed service exceeding pre-approved cost levels is also required to be submitted to the Audit Committee for specific approval.

The Audit Committee will revise the list of general pre-approved services from time to time based on subsequent determinations. The Audit Committee does not delegate its responsibilities to pre-approve services performed by the independent auditor to management.

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PART IV

|ITEM 15. | EXHIBITS   AND FINANCIAL STATEMENT SCHEDULES
|-------- | --------------------------------------------

|EXHIBIT   NO. |  | DESCRIPTION                                                                                                                                
|------------- |  | -------------------------------------------------------------------------------------------------------------------------------------------
|              |  |                                                                                                                                            
|31.1          |  | Certification Pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended.   Filed herewith.                 
|31.2          |  | Certification Pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended.   Filed herewith.                 
|32.1          |  | Certification Pursuant to   18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the   Sarbanes-Oxley Act of 2002. Filed herewith.
|32.2          |  | Certification Pursuant to   18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the   Sarbanes-Oxley Act of 2002. Filed herewith.

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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.

|                 | AMTECH SYSTEMS, INC.
|---------------- | --------------------
|                 |                     
|January 29, 2007 | By:                 
|                 |                     
|                 |                     

Pursuant to the requirements of the Securities Exchange Act of 1934, this report on Form 10-K/A 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/ Jong S. Whang                         |       | Chairman of the Board,   President |     
|          |                                           |       | and Chief Executive   Officer      |     
|          | Jong S. Whang                             |       | (Principal Executive   Officer)    |     
|          |                                           |       |                                    |     
|          | /s/ Bradley C. Anderson                   |       | Vice President  Finance   and     |     
|          |                                           |       | Chief Financial Officer            |     
|          | Bradley C. Anderson                       |       | (Principal Financial   Officer)    |     
|          |                                           |       |                                    |     
|          | /s/ Robert T. Hass                        |       | Chief Accounting Officer           |     
|          |                                           |       | (Principal Accounting   Officer)   |     
|          | Robert T. Hass                            |       |                                    |     
|          |                                           |       |                                    |     
|          | *                                         |       | Director                           |     
|          |                                           |       |                                    |     
|          | Lawrence D. Firestone                     |       |                                    |     
|          |                                           |       |                                    |     
|          | *                                         |       | Director                           |     
|          |                                           |       |                                    |     
|          | Robert F. King                            |       |                                    |     
|          |                                           |       |                                    |     
|*By:      | /s/ Bradley C. Anderson                   |       |                                    |     
|          |                                           |       |                                    |     
|          | Bradley C. Anderson,   Attorney-In-Fact** |       |                                    |     

|                                                                                                                          
|--------------------------------------------------------------------------------------------------------------------------
|**By authority of the   power of attorney filed as Exhibit 24 to the Annual Report on Form 10-K filed   December 21, 2006.

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EXHIBIT INDEX

|EXHIBIT   NO. |  | DESCRIPTION                                                                                                                                
|------------- |  | -------------------------------------------------------------------------------------------------------------------------------------------
|              |  |                                                                                                                                            
|31.1          |  | Certification Pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended.   Filed herewith.                 
|31.2          |  | Certification Pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended.   Filed herewith.                 
|32.1          |  | Certification Pursuant to   18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the   Sarbanes-Oxley Act of 2002. Filed herewith.
|32.2          |  | Certification Pursuant to   18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the   Sarbanes-Oxley Act of 2002. Filed herewith.

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