In Switzerland, the Opalinus Clay formation is considered the most likely host rock for a deep geological repository for nuclear waste. In deep geological repositories, H2 is expected to be the most abundant gas formed from the degradation of waste and from metal corrosion. The microbial community present in Opalinus Clay is capable of utilizing H2 as an electron donor and sulfate as an electron acceptor to produce hydrogen sulfide. This could be problematic due to its potential for increasing the corrosion of metal waste canisters containing radioactive waste, however, the possible impacts of these processes on the clay rock have not been fully investigated. In this study, a series of microcosm experiments were set-up containing Opalinus Clay and porewater from the Mont Terri underground research laboratory (Switzerland) as an inoculum. Uninoculated microcosms were established to investigate abiotic processes. In the presence of clay, a higher aqueous sulfate concentration was detected than in those with only porewater present and this concentration decreased over time in the inoculated experiments. However, there was no evidence of hydrogen sulfide production in the aqueous phase. In all experiments with clay, there was an increase in aqueous Fe2+ concentrations with the highest concentrations found in uninoculated experiments. The sulfur speciation of the Opalinus Clay was analysed and the results of the inoculated sample suggested that hydrogen sulfide reacted with Fe2+, precipitating iron sulfide minerals. After the incubation period, the microbial community was dominated by the sulfate-reducing Desulfobulbaceae family. The study suggests that H2-fuelled, microbially-mediated sulfate reduction can affect the mineral composition within the Opalinus Clay due to the precipitation of iron sulfide minerals. These precipitation reactions may enhance the long-term integrity of the repository by removing corrosive hydrogen sulfide from solution when sufficient Fe2+ is available and so protecting the canisters containing the nuclear waste.