Biogas upgrading is an expanding field dealing with the increase in methane content of the biogas to produce biomethane. Biomethane has a high calorific content and can be used as a vehicle fuel or directly injected into the gas grid. Bioelectrochemical systems (BES) could become an alternative for biogas upgrading, by which the yield of the process in terms of carbon utilisation could be increased. The simulated effluent from a water scrubbing-like unit was used to feed a BES. The BES was operated with the biocathode poised at −800 mV vs. SHE to drive the reduction of the CO2 fraction of the biogas into methane. The BES was operated in batch mode to characterise methane production and under continuous flow to demonstrate its long-term viability. The maximum methane production rate obtained during batch tests was 5.12 ± 0.16 mmol m−2 per day with a coulombic efficiency (CE) of 75.3 ± 5.2%. The production rate increased to 15.35 mmol m−2 per day (CE of 68.9 ± 0.8%) during the continuous operation. Microbial community analyses and cyclic voltammograms showed that the main mechanism for methane production in the biocathode was hydrogenotrophic methanogenesis byMethanobacterium sp., and that electromethanogenesis occurred to a minor extent. The presence of other microorganisms in the biocathode, such as Methylocystis sp. revealed the presence of side reactions, such as oxygen diffusion from the anode compartment, which decreased the efficiency of the BES. The results of the present work offer the first experimental report on the application of BES in the field of biogas upgrading processes.