Selected Quarterly Data (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended								12 Months Ended
	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2010	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2010
Selected Quarterly Data (Unaudited) [Abstract]
Revenue	$ 10,945	$ 24,300	$ 21,566	$ 24,728	$ 59,868	$ 71,871	$ 61,253	$ 53,712	$ 81,539	$ 246,705	$ 120,019
Gross margin	(6,860)	4,804	4,048	7,201	20,242	26,116	24,703	19,597	9,193	90,657	42,712
Provision for income taxes	(3,670)	(1,110)	(220)	(320)	2,600	5,160	5,100	3,330	(5,320)	16,190	6,150
Net income (loss) attributable to Amtech Systems, Inc.	(14,111)	(2,965)	(5,079)	(876)	3,075	7,298	7,517	4,992	(23,031)	22,882	9,563
Comprehensive income attributable to Amtech Systems, Inc.	$ (13,470)	$ (6,816)	$ (2,877)	$ (4,607)	$ (1,927)	$ 8,744	$ 11,430	$ 3,539	$ (32,451)	$ 20,983	$ 7,920
Basic	$ (1.49)	$ (0.31)	$ (0.54)	$ (0.09)	$ 0.32	$ 0.76	$ 0.79	$ 0.54	$ (2.43)	$ 2.41	$ 1.06
Shares used in calculation	9,482	9,479	9,479	9,446	9,581	9,576	9,487	9,278	9,471	9,480	9,022
Diluted	$ (1.49)	$ (0.31)	$ (0.54)	$ (0.09)	$ 0.31	$ 0.74	$ 0.77	$ 0.52	$ (2.43)	$ 2.34	$ 1.04
Shares used in calculationi	9,482	9,479	9,479	9,446	9,778	9,852	9,781	9,609	9,471	9,764	9,237