Earnings Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended			6 Months Ended
	Mar. 31, 2016	Mar. 31, 2015	Dec. 31, 2014	Mar. 31, 2016	Mar. 31, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (1,499)	$ (2,321)	$ (2,321)	$ (5,513)	$ (7,515)
Weighted average shares outstanding (in shares)	13,169,000	11,997,000	11,997,000	13,161,000	10,914,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.11)	$ (0.19)	$ (0.19)	$ (0.42)	$ (0.69)
Diluted shares (in shares)	13,169,000	11,997,000	11,997,000	13,161,000	10,914,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.11)	$ (0.19)	$ (0.19)	$ (0.42)	$ (0.69)
Stock Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,906,000	1,746,000		1,906,000	1,746,000
Restricted Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount		14,000			14,000