Earnings Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (1,209)	$ (1,604)	$ (6,722)	$ (9,119)
Weighted average shares outstanding (in shares)	13,173,000	13,103,000	13,165,000	11,644,000
Basic loss per share attributable to Amtech shareholders (dollars per share)	$ (0.09)	$ (0.12)	$ (0.51)	$ (0.78)
Diluted shares (in shares)	13,173,000	13,103,000	13,165,000	11,644,000
Diluted loss per share attributable to Amtech shareholders (dollars per share)	$ (0.09)	$ (0.12)	$ (0.51)	$ (0.78)
Stock Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share (in shares)	1,840,000	1,640,000	1,840,000
Restricted Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share (in shares)				14,000