The process of anaerobic digestion producing biogas is an eco-friendly energy source that promotes recycling from waste biomass such as food chain residues, wet waste, wastewater. In this study, we focused on the problem of the sulfide (H2S) produced by the sulfate-reducing bacteria (SRB) in the presence of sulfate residues. This byproduct is dangerous for human health and an issue due to the highly corrosive effect on metallic components. To this purpose, the Molybdate, a sulfate analog, known in the literature to inhibit SRBs by blocking the first enzyme of the metabolic pathway of anaerobic respiration, was applied. The experiments carried out showed that a concentration of 0.3 mM of molybdate was enough to inhibit the SRB in a complex environment of the anaerobically digested sludge (ADS) took from a real biogas producing bioreactor. During the study, we observed the importance of the sulfate concentration sulfate in the system. Indeed, the production of sulfide was stopped only under the threshold ratio value of 1:10 (molybdate: sulfate). In the short term, the addition of molybdate did not alter the production and quality (% of methane) of the biogas, nor the anaerobic microbial community, including SRB population itself.