Earnings Per Share & Diluted Earnings Per Share - Reconciliation of Denominators of Basic and Diluted EPS Calculations (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2017
Numerator:
Net income from continuing operations	$ 982	$ 893	$ 1,012	$ 248	$ (1,110)	$ 4,979	$ 1,061	$ 1,701	$ 3,135	$ 6,631	$ 2,194
Net (loss) income from discontinued operations	$ (184)	$ 1,154	$ (6,647)	$ (2,620)	$ (7,843)	$ (8)	$ 1,774	$ 4,751	(8,297)	(1,326)	5,892
Net loss from non-controlling interest - discontinued operations											1,045
Net (loss) income attributable to Amtech Systems, Inc.									$ (5,162)	$ 5,305	$ 9,131
Denominator:
Weighted-average shares used to compute basic EPS	14,266	14,245	14,228	14,220	14,730	14,925	14,891	14,781	14,240	14,833	13,378
Common stock equivalents									35	232	123
Weighted-average shares used to compute diluted EPS	14,304	14,316	14,258	14,252	14,730	15,091	15,154	15,298	14,275	15,065	13,501
Basic income per share from continuing operations	$ 0.07	$ 0.06	$ 0.07	$ 0.02	$ (0.08)	$ 0.33	$ 0.07	$ 0.12	$ 0.22	$ 0.45	$ 0.16
Basic (loss) income per share from discontinued operations	(0.01)	0.08	(0.47)	(0.18)	(0.53)	0.00	0.12	0.32	(0.58)	(0.09)	0.52
Net (loss) income per basic share	0.06	0.14	(0.40)	(0.16)	(0.61)	0.33	0.19	0.44	(0.36)	0.36	0.68
Diluted income per share from continuing operations	0.07	0.06	0.07	0.02	(0.08)	0.33	0.07	0.11	0.22	0.44	0.16
Diluted (loss) income per share from discontinued operations	(0.01)	0.08	(0.47)	(0.18)	(0.53)	0.00	0.12	0.31	(0.58)	(0.09)	0.52
Net (loss) income per diluted share	$ 0.06	$ 0.14	$ (0.40)	$ (0.16)	$ (0.61)	$ 0.33	$ 0.19	$ 0.42	$ (0.36)	$ 0.35	$ 0.68