|            |
|------------|
|            |  |  |
| (Mark One) |   |   |
| [X]        |   | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|       |   | For the fiscal year ended: September 30, 2016 |
|       |   | OR |
| [  ]       |   | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|       |   | For the transition period from ________________ to ________________ |

|                                                        |
|--------------------------------------------------------|
|                                                        |  |
| AMTECH SYSTEMS, INC.                                   |
| (Exact name of registrant as specified in its charter) |

|                                                               |
|---------------------------------------------------------------|
|                                                               |  |
| Arizona                                                       | 86-0411215 |
| (State or other jurisdiction ofincorporation or organization) | (I.R.S. EmployerIdentification 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, $0.01 Par Value                                          |
| (Title of Class)                                                       |

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|                   |
|-------------------|
|                   |  |
|              | /s/ MAYER HOFFMAN MCCANN P.C. |
| Phoenix, Arizona  |   |
| November 30, 2016 |   |

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|                   |
|-------------------|
|                   |  |
|              | /s/ MAYER HOFFMAN MCCANN P.C. |
| Phoenix, Arizona  |   |
| November 30, 2016 |   |

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|                  |
|------------------|
|                  |  |  |  |
|             |
|             |   |   |   |
|             | AMTECH SYSTEMS, INC. |
|             |   |
| December 1, 2016 | By:        | /s/ Robert T. Hass |   |
|             |   | Robert T. Hass, Executive Vice President - |   |
|             |   | Finance and Chief Financial Officer |   |
|             |   |   |   |

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|                                                                                                                                                                                   |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|                                                                                                                                                                                   |  |  |  |  |
| SIGNATURE                                                                                                                                                                         |   | TITLE |   | DATE |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Executive Chairman and |   | December 1, 2016 |
| Jong S. Whang                                                                                                                                                                     |   | Chairman of the Board |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Chief Executive Officer |   | December 1, 2016 |
| Fokko Pentinga                                                                                                                                                                    |   | and President |   |   |
|                                                                                                                                                                              |   | (Principal Executive Officer) |   |   |
|                                                                                                                                                                              |   |   |   |   |
|  /s/ Robert T. Hass                                                                                                                                                          |   | Executive Vice President – Finance and Chief Financial Officer |   | December 1, 2016 |
| Robert T. Hass                                                                                                                                                                    |   | (Principal Financial and Accounting Officer) |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Director |   | December 1, 2016 |
| Robert M. Averick                                                                                                                                                                 |   |   |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Director |   | December 1, 2016 |
| Michael Garnreiter                                                                                                                                                                |   |   |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Director |   | December 1, 2016 |
| Paul J. van der Wansem                                                                                                                                                            |   |   |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Director |   | December 1, 2016 |
| Egbert J.G. Goudena                                                                                                                                                               |   |   |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Director |   | December 1, 2016 |
| Robert F. King                                                                                                                                                                    |   |   |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *                                                                                                                                                                                 |   | Director |   | December 1, 2016 |
| Sukesh Mohan                                                                                                                                                                      |   |   |   |   |
|                                                                                                                                                                              |   |   |   |   |
| *By: /s/ Robert T. Hass                                                                                                                                                           |   |   |   |   |
| Robert T. Hass, Attorney-In-Fact**                                                                                                                                                |   |   |   |   |
|                                                                                                                                                                              |   |   |   |   |
| **By authority of the power of attorney previously filed as Exhibit 24.1 with the registrant's annual report on Form 10-K for the fiscal year ended September 30, 2016. |