Earnings Per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended
	Dec. 31, 2013		Dec. 31, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (794)		$ (4,194)
Weighted average shares outstanding (in shares)	9,560,000		9,494,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.08)		$ (0.44)
Common stock equivalents (in shares)	0	[1]	0	[1]
Diluted shares (in shares)	9,560,000		9,494,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.08)		$ (0.44)
Stock Options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,275,000		1,205,000
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

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