Sulfidation is a key process for silver nanoparticles released from consumer products in the environment. This study focuses on the impact of a model soil microorganism, Bacillus subtilis, on the fate of pristine and already sulfidized Ag-NPs. The nanoparticles were incubated with the initial growth medium, isolated secretome, and living bacteria, and characterized for their size and morphology, agglomeration state, structure, and Ag speciation. No Ag internalization or sorption on the cell wall was detected. A partial sulfidation, leading to an Ag-Ag2S core-shell structure, was observed in the presence of the secretome, and the rate limiting step of the reaction was the oxidation of Ag0, and it was favored near the crystal dislocations. The sulfidation was complete in the presence of the living bacteria and followed an indirect pathway. Both crystalline Ag2S and amorphous Ag2S and/or Ag-thiol were identified. At the opposite, the bacteria had no impact on Ag2S. These results suggest that microorganisms participate in the sulfidation of Ag-NPs in aerobic systems such as unsaturated soils, and thus affect the bioavailability of Ag. It is important to take these transformations into account during exposure experiments, since they drastically change the exposure conditions. Finally, the secretome of B. subtilis might be used for the green synthesis of Ag-Ag2S core-shell nanoparticles.