Dark fermentation of cheese whey (CW) for the production of biohydrogen generates an acidic effluent, containing high concentrations of volatile fatty acids, which needs to be further treated before disposal and possibly further valorised. This study develops a dual-chamber Microbial Electrolysis Cell (MEC) that achieves simultaneously the reduction of the organic content of this effluent to environmentally acceptable levels, along with bio-electrochemical reduction of CO2 to CH4. The MEC was operated for 140 days and the effect of the following conditions on the MEC performance was examined: (a) the feed concentration of the acidic fermentate (in the range 6–81 gCOD/L), (b) the conductivity of the feed modified via KCl addition (range 2–22 mS/cm), (c) the MEC operation mode (with or without catholyte renewal) and (d) the solids content (modified via CW filtration prior to its use). The results showed that high COD removal (>95 %) was achieved in all cases, along with a CH4 production of up to 1.1 mmol/gCODconsumed. The best performance of the cell was obtained for a feed COD concentration of ∼30 gCOD/L and a feed conductivity of ∼15 mS/cm; these conditions resulted in a COD removal exceeding 99 %, a CH4 production of 1.1 mmolCH4/gCODconsumed and a net energy production of 15.8 % compared to the energy demand of the system. The electrochemical study of the system revealed that higher and lower feed COD concentrations were characterized by higher internal resistances. The results indicate that the MEC can be exploited for further treatment and valorization of a high-strength effluent along with the production of CH4 with an energy surplus, as an efficient waste-to-energy technology.