Earnings Per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended				6 Months Ended
	Mar. 31, 2013		Mar. 31, 2012		Mar. 31, 2013	Mar. 31, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (2,092)		$ (5,079)		$ (6,285)	$ (5,955)
Weighted average shares outstanding (in shares)	9,539,000		9,479,000		9,516,000	9,462,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.22)		$ (0.54)		$ (0.66)	$ (0.63)
Common stock equivalents (1) (in shares)	0	[1]	0	[1]	0	0
Diluted shares (in shares)	9,539,000		9,479,000		9,516,000	9,462,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.22)		$ (0.54)		$ (0.66)	$ (0.63)
Stock Options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,200,000		896,000		1,200,000	896,000
Restricted Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	72,000		135,000		72,000	135,000

[1] The number of common stock equivalents is calculated using the treasury stock method and the average market price during the period.