Earnings Per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended				6 Months Ended
	Mar. 31, 2014		Mar. 31, 2013		Mar. 31, 2014		Mar. 31, 2013
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (3,751)		$ (2,092)		$ (4,545)		$ (6,285)
Weighted average shares outstanding (in shares)	9,679,000		9,539,000		9,619,000		9,516,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.39)		$ (0.22)		$ (0.47)		$ (0.66)
Common stock equivalents (in shares)	0	[1]	0	[1]	0	[1]	0	[1]
Diluted shares (in shares)	9,679,000		9,539,000		9,619,000		9,516,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.39)		$ (0.22)		$ (0.47)		$ (0.66)
Stock Options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,016,000		1,202,000		1,016,000		1,202,000
Restricted Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	38,000		72,000		38,000		72,000

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