Earnings Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended
	Dec. 31, 2015	Dec. 31, 2014
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (4,015)	$ (5,195)
Weighted average shares outstanding (in shares)	13,152,000	9,854,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.31)	$ (0.53)
Common stock equivalents (in shares)	0	0
Diluted shares (in shares)	13,152,000	9,854,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.31)	$ (0.53)
Stock Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,938,000	1,346,000
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