The microbial fuel cells (MFCs) are the focus of extensive investigation as one of the promising technologies for renewable energy generation and wastewater treatment. Two-chambered MFCs were designed to investigate the removal of metronidazole and to quantify the effect of antibiotic on the efficacy of energy generation. Using 1,000 mg glucose L−1 containing different concentrations of metronidazole (0, 10, 30, 50 mg L−1) as the fuels, the corresponding power densities were 141.94, 99.23, 25.44, 16.26 mW m−2, respectively. The adverse effect on the performance of the MFCs was reversible. The removal of metronidazole achieved 85.4% within 24 hours in MFCs, while only 35.2% in open circuit. Current generation could account for the improved removal efficiency at these tested concentration levels. The findings of this paper indicated that antibiotics such as metronidazole could be removed in MFCs, which has implications for general wastewater treatment.