Earnings Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (53)	$ (4,015)
Weighted average shares outstanding (in shares)	13,179,000	13,152,000
Basic loss per share attributable to Amtech shareholders (USD per share)	$ 0.00	$ (0.31)
Diluted shares (in shares)	13,179,000	13,152,000
Diluted loss per share attributable to Amtech shareholders (USD per share)	$ 0.00	$ (0.31)
Stock Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share (in shares)	1,886,000	1,938,000