Abstract Bio-based waste management processes, as anaerobic digestion, couple waste treatment with energy production using natural processes based on microbial metabolism. Microbial fuel cells (MFCs) combine the production of electric power to the lowering the load of waste organic and mineral nutrients. In this study, the coordinated utilization of MFCs with anaerobic digestion in a two-steps process has been investigated. A single chamber, air cathode, membraneless MFCs with graphite plates as electrodes, fed with the organic fraction of municipal waste, was run for 4 weeks. The energy obtained was characterized by a maximum current density of 42.3 mA/m2 kg, a power density of 1.98 mW/m2 kg, and a columbic efficiency ηC ∼5%. pH of the slurry was maintained at 6.8 ± 0.9 along the experiment. MFC spent substrate was then used in a batch experiment for biohydrogen and biomethane production through AD. The biohydrogen increased by 276%, as compared to that produced from the same fresh untreated Organic Fraction of Municipal Solid Waste. A decrease in methane production of 66% was however observed. The analysis of MFC spent substrate revealed the prevalence of Lactobacillaceae, Bacillaceae, Clostridia and Pseudomonadaceae, with Pseudomonas aeruginosa colonizing the cathode.