Decreasing environmental pollution is one of the most important research problems. In this study, a simple and environmentally friendly approach is presented to decorate reduced graphene oxide with Ag nanoparticles (Ag/rGO nanocomposites) in situ using only Shewanella oneidensis MR-1 as the reducing agent. The results indicate the successful growth of Ag nanoparticles (NPs) with a diameter < 10 nm on rGO without aggregation. Ag/rGO nanocomposites showed a remarkable sterilization capacity (up to 99.9%) when used at a concentration of 2 mg/L aqueous solution against Gram-negative Escherichia coli over 15 min, which is attributed to the rapid release of Ag ions sites that enhances the bacteria-bactericide interaction and the trapping of bacteria by the Ag/rGO. In addition, the catalytic degradation ratio of p-nitrophenol (4-NP) in the presence of Ag/rGO synergistic with S. oneidensis MR-1 reaches 98.2% after 10 min of reaction. Fluorescence experiments confirm that the maximum amount of reactive oxygen species is released in the synergistic process, and thus, Ag/rGO combined with S. oneidensis MR-1 show the best catalytic reduction ability.