Microbial fuel cells (MFCs) are emerging wastewater treatment systems with a proven potential for denitrification. In this study, we have developed a high-rate denitrifying MFC. The anode consisted of cow manure and fruit waste and the cathode consisted of cow manure and soil. The initial chemical oxygen demand (COD)/nitrate nitrogen (NO3 −-N) was varied from 2 to 40 at the cathode while keeping the anode ratio fixed at 100. NO3 −-N removal rate of 7.1 ± 0.9 kg NO3 −-N/m3 net cathodic compartment (NCC)/day was achieved at cathode COD/NO3 −-N ratio 7.31 with the current density of 190 ± 9.1 mA/m2 and power density of 31.92 ± 4 mW/m2 of electrode surface area. We achieved an open-circuit voltage (OCV) of 410 ± 20 mV at initial cathodic NO3 −-N of 0.345 g/l. The cathode COD/NO3 −-N ratio had a significant influence on MFC’s OCV and nitrate removal rate. Lower OCV (<150 mV) and NO3 −-N removal rates were observed at COD/NO3 −-N ratio >12 and <7. Experiments done at different cathode pH values indicated that the optimum pH for denitrification was 7. Under optimized biochemical conditions, nitrate removal rate of 6.5 kg NO3 −-N/m3 net cathodic compartment (NCC)/day and power density of 210 mW/m2 were achieved in a low resistance MFC. The present study thus demonstrates the utility of MFCs for the treatment of high nitrate wastes. © 2016, Springer-Verlag Berlin Heidelberg.