Earnings Per Share & Diluted Earnings Per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2014
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net loss attributable to Amtech Systems, Inc.	$ (285)	$ (1,209)	$ (1,499)	$ (4,015)	$ 1,349	$ (1,604)	$ (2,321)	$ (5,195)	$ (7,008)	$ (7,771)	$ (13,047)
Weighted average shares outstanding (in shares)	13,177	13,173	13,169	13,152	13,150	13,103	11,997	9,854	13,168	12,022	9,732
Basic loss per share attributable to Amtech shareholders (dollars per share)	$ (0.02)	$ (0.09)	$ (0.11)	$ (0.31)	$ 0.10	$ (0.12)	$ (0.19)	$ (0.53)	$ (0.53)	$ (0.65)	$ (1.34)
Weighted average shares outstanding, common stock equivalents (in shares)									0	0	0
Weighted average shares outstanding, diluted shares (in shares)	13,177	13,173	13,169	13,152	13,259	13,103	11,997	9,854	13,168	12,022	9,732
Diluted loss per share attributable to Amtech shareholders (dollars per share)	$ (0.02)	$ (0.09)	$ (0.11)	$ (0.31)	$ 0.10	$ (0.12)	$ (0.19)	$ (0.53)	$ (0.53)	$ (0.65)	$ (1.34)
Stock Options and Restricted Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from the computation of earnings per share									1,840	1,640	1,099