The major objective of the EU Horizon 2020 project “BioMOre” is the technical realization of indirect in situ leaching of Kupferschiefer sandstone and black shale ore by a ferric iron lixiviant generated by a mixed culture of autotrophic, acidophilic, iron-oxidizing bacteria and archaea in a ferric iron-generating bioreactor (FIGB). These organisms could colonize the deeply buried geological formations even under anaerobic conditions as most are able to grow by coupling the reduction of ferric iron to the oxidation of reduced sulfur compounds in the absence of oxygen. Development of an inhibition protocol to eliminate these allochthonous microbial bioreactor populations subsequent to the completion of in situ bioleaching was therefore investigated. Column bioleaching experiments using a laboratory-scale FIGB confirmed not only that metals were solubilised from both the sandstone and shale ores, but also that significant numbers of bacteria were released from the FIGB. The efficacy of 13 different chemical compounds in inhibiting microbial iron oxidation has been tested at different concentrations in shake flask and FIGB-coupled columns. Iron-oxidation activity, microcalorimetrically-determined activity and ATP measurements, in combination with microscopic cell counts and biomolecular analysis (T-RFLP, qPCR), plate counts and most-probable-number (MPN), were used to monitor the inhibiting effects on the acidophiles. Complete inhibition of metabolic activity of iron-oxidizing acidophiles was achieved in the presence of 0.4 mM formate, 300 mM chloride, 100 mM nitrate, 10 mM of primary C6 to C8 alcohols, 100 mM 1-butanol, 100 mM 1-pentanol, 0.1 mM SDS or 0.35 mM benzoic acid. No inhibition was found for 0.6 mM acetic acid and 200 mM methanol. Based on these results a recipe for the chemical composition of the “decommissioning solution” is proposed.