Selected Quarterly Data (Unaudited) (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended								12 Months Ended
	Sep. 30, 2014	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2012
Selected Quarterly Data (Unaudited) [Abstract]
Revenue	$ 19,822	$ 9,190	$ 12,717	$ 14,772	$ 6,925	$ 10,398	$ 8,118	$ 9,357	$ 56,501	$ 34,798	$ 81,539
Gross margin	2,562	1,631	2,898	4,535	3,159	(2,677)	2,453	1,378	11,626	4,313	9,193
Provision for income taxes	(645)	1,325	0	560	580	2,560	(800)	(480)	1,240	1,860	(5,320)
Net loss attributable to Amtech Systems, Inc.	(3,245)	(5,257)	(3,751)	(794)	(1,682)	(12,101)	(2,092)	(4,194)	(13,047)	(20,069)	(23,031)
Comprehensive loss attributable to Amtech Systems, Inc.	$ (4,892)	$ (5,568)	$ (3,756)	$ (66)	$ (75)	$ (11,387)	$ (3,555)	$ (2,791)	$ (15,491)	$ (19,482)	$ (32,451)
Basic (dollars per share)	$ (0.33)	$ (0.53)	$ (0.39)	$ (0.08)	$ (0.18)	$ (1.27)	$ (0.22)	$ (0.44)	$ (1.34)	$ (2.11)	$ (2.43)
Shares used in calculation	9,846	9,843	9,679	9,560	9,543	9,539	9,539	9,494	9,732	9,529	9,471
Diluted (dollars per share)	$ (0.33)	$ (0.53)	$ (0.39)	$ (0.08)	$ (0.18)	$ (1.27)	$ (0.22)	$ (0.44)	$ (1.34)	$ (2.11)	$ (2.43)
Shares used in calculation	9,846	9,843	9,679	9,560	9,543	9,539	9,539	9,494	9,732	9,529	9,471