Selected Quarterly Data (Unaudited) (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2013
Selected Quarterly Data (Unaudited) [Abstract]
Revenue	$ 28,198	$ 40,016	$ 24,273	$ 12,396	$ 19,822	$ 9,190	$ 12,717	$ 14,772	$ 104,883	$ 56,501	$ 34,798
Gross margin	6,563	10,128	6,889	3,428	2,562	1,631	2,898	4,535	27,008	11,626	4,313
Provision for (benefit of) for income taxes	1,270	290	170	180	(645)	1,325	0	560	1,910	1,240	1,860
Net income (loss) attributable to Amtech Systems, Inc.	1,349	(1,604)	(2,321)	(5,195)	(3,245)	(5,257)	(3,751)	(794)	(7,771)	(13,047)	(20,069)
Comprehensive income (loss) attributable to Amtech Systems, Inc.	$ 1,414	$ (1,344)	$ (4,470)	$ (6,247)	$ (4,892)	$ (5,568)	$ (3,756)	$ (66)	$ (9,727)	$ (15,491)	$ (19,482)
Basic (dollars per share)	$ 0.10	$ (0.12)	$ (0.19)	$ (0.53)	$ (0.33)	$ (0.53)	$ (0.39)	$ (0.08)	$ (0.65)	$ (1.34)	$ (2.11)
Shares used in calculation	13,150	13,103	11,997	9,854	9,846	9,843	9,679	9,560	12,022	9,732	9,529
Diluted (dollars per share)	$ 0.10	$ (0.12)	$ (0.19)	$ (0.53)	$ (0.33)	$ (0.53)	$ (0.39)	$ (0.08)	$ (0.65)	$ (1.34)	$ (2.11)
Shares used in calculation	13,259	13,103	11,997	9,854	9,846	9,843	9,679	9,560	12,022	9,732	9,529