Selected Quarterly Data (unaudited) (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended								12 Months Ended
	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2011
Selected Quarterly Data (Unaudited) [Abstract]
Revenue	$ 6,925	$ 10,398	$ 8,118	$ 9,357	$ 10,945	$ 24,300	$ 21,566	$ 24,728	$ 34,798	$ 81,539	$ 246,705
Gross margin	3,159	(2,677)	2,453	1,378	(6,860)	4,804	4,048	7,201	4,313	9,193	90,657
Provision for income taxes	580	2,560	(800)	(480)	(3,670)	(1,110)	(220)	(320)	1,860	(5,320)	16,190
Net loss attributable to Amtech Systems, Inc.	(1,682)	(12,101)	(2,092)	(4,194)	(14,111)	(2,965)	(5,079)	(876)	(20,069)	(23,031)	22,882
Comprehensive loss attributable to Amtech Systems, Inc.	$ (75)	$ (11,387)	$ (3,555)	$ (2,791)	$ (13,470)	$ (6,816)	$ (2,877)	$ (4,607)	$ (19,482)	$ (32,451)	$ 20,983
Basic (dollars per share)	$ (0.18)	$ (1.27)	$ (0.22)	$ (0.44)	$ (1.49)	$ (0.31)	$ (0.54)	$ (0.09)	$ (2.11)	$ (2.43)	$ 2.41
Shares used in calculation	9,543	9,539	9,539	9,494	9,482	9,479	9,479	9,446	9,529	9,471	9,480
Diluted (dollars per share)	$ (0.18)	$ (1.27)	$ (0.22)	$ (0.44)	$ (1.49)	$ (0.31)	$ (0.54)	$ (0.09)	$ (2.11)	$ (2.43)	$ 2.34
Shares used in calculation	9,543	9,539	9,539	9,494	9,482	9,479	9,479	9,446	9,529	9,471	9,764