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Growing energy needs and rising concern about fossil fuel emissions and climate change have directed research towards alternative fuels and energy producing technologies. Hydrogen fuel is exhibiting perhaps the best potential as an alternative energy carrier and source to conventional fossil fuels. Microbial Electrolysis Cell (MEC) is a potential attractive green technology for clean, sustainable hydrogen production from wastewater. The MEC consist of anaerobic anode and cathode chamber separated by proton exchange membrane. The microbes oxidized the organic matter from the substrate and releases protons, electrons which are transferred and combined in the cathode to produce hydrogen with the help of small voltage supply. Anaerobic Digester is well proven technology for biogas production. The main aim of the present objective was to improve the hydrogen and biogas production and substrate removal efficiency by integrating of MEC with anaerobic Digester into MEC. Activated sludge as a biocatalyst and ethanol as carbon source for the system. The MEC performance was investigated with respect to applied voltage and substrate concentration. The MEC performance in terms of hydrogen and biogas generation, treatment efficiency was investigated in this study. The results of this experiments showed that the MFC performance in terms of hydrogen production as well as treatment efficiency was significantly improved.