Earnings Per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended
	Dec. 31, 2012		Dec. 31, 2011
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (4,194)		$ (876)
Weighted average shares outstanding (in shares)	9,494,000		9,446,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.44)		$ (0.09)
Common stock equivalents (1) (in shares)	0	[1]	0	[1]
Diluted shares (in shares)	9,494,000		9,446,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.44)		$ (0.09)
Stock Options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,205,000		900,000
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

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