A sustainable clean energy production from oxidation of biodegradable materials was carried out in a microbial fuel cell (MFC) stack consisting of four MFC units. The stack was fabricated and tested for its scalability using a high engineering, low oxygen mass transfer membrane; namely, sulfonated poly ether ether ketone. Sodium acetate was used as the substrate and dairy waste inoculum was utilized as biocatalyst for power generation. Maximum current and power density generation produced in the MFC stack were 1033 mA m−2 and 826 mW m−2, respectively, with a columbic efficiency of 58%. Impedance spectroscopy demonstrated the internal resistance distribution in a single unit cell of the MFC stack and indicated a much lower resistance of 8.5 Ω. Cyclic voltammetry revealed that the enrichment of culture and partial anodic biofilm mixture increased the electrochemical activity. Additionally, experiments were performed with dairy wastewater which produced a moderate current and power density of 672 mA m−2 and 640 mW m−2, respectively. The MFC stack system demonstrated the ability to treat real wastewater with the added benefit of harvesting electricity energy. © 2015 American Institute of Chemical Engineers Environ Prog, 35: 80–87, 2016