Earnings Per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended				9 Months Ended
	Jun. 30, 2014		Jun. 30, 2013		Jun. 30, 2014		Jun. 30, 2013
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (5,257)		$ (12,101)		$ (9,802)		$ (18,386)
Weighted average shares outstanding (in shares)	9,843,000		9,539,000		9,694,000		9,524,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.53)		$ (1.27)		$ (1.01)		$ (1.93)
Common stock equivalents (in shares)	0	[1]	0	[1]	0	[1]	0	[1]
Diluted shares (in shares)	9,843,000		9,539,000		9,694,000		9,524,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.53)		$ (1.27)		$ (1.01)		$ (1.93)
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		1,064,000
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		38,000

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