The H2020 BioMOre project (www.biomore.info, Grant Agreement #642456) tests the feasibility of in-situ bioleaching of copper in deep subsurface deposits in the Rudna Mine, Poland. Copper is leached using biologically produced ferric iron solution, which is recycled back to the in-situ reactor after re-oxidation by iron-oxidizing bacteria (IOB). From a post operational point of view, it is important that the biological processes applied during the operation can be controlled and terminated. Our goal was to determine the possibility to use natural saline mine water for the inactivation of introduced IOB remaining in the in-situ reactor after completion of the leaching process of the Kupferschiefer ore. Aerobic and anaerobic microcosms containing acid-leached (pH 2) sandstone or black shale from the Kupferschiefer in the Rudna mine were further leached with the effluent from an iron-oxidizing bioreactor, at a temperature of 30°C, for 10 days, to simulate in-situ leaching. After the removal of the iron solution, residing IOB were inactivated by filling the microcosms with saline water (65 g L
-) originating from the mine. The saline water completely inactivated the IOB and the naturally occurring saline water of the mine can be used for long-term post process inactivation of bioleaching microorganisms.