Advanced oxidation processes (AOPs) have been intensely studied for the removal of refractory pollutants because of the strong oxidizing capacity of hydroxyl radical. One of the emerging AOP methods gaining increased attention is bio-electro-Fenton (BEF) which can generate hydroxyl radical in-situ in the cathode chamber using the energy harvested by exoelectrogenic bacteria in the anode. In this study, the feasibility of BEF technology for the removal of metoprolol, a typical micropollutant widely found in the water environment, was for the first time investigated. It was found that applied voltage and working pH had a significant effect on removal efficiency while Fe2+ dosage as catalyst showed a little effect. Besides removal by hydroxyl radical, metoprolol might be absorbed on the surface of the reactor, electrode, and precipitated with iron sludge, especially at neutral pH. In a batch experiment with a supplied voltage of 0.2 V, pH 3, and a Fe2+ dose of 0.2 mM, the removal rate of metoprolol in the BEF for the synthetic wastewater and the real effluent from the secondary sediment tank was 66% and 55% within 12 h, respectively. A possible degradation pathway was proposed. Then the removal of metoprolol in a continuous flow BEF system was further studied at different hydraulic retention times (HRTs) of 2, 4, and 6 h, about 77%, 92%, and 95% removal was observed. A toxicity test (less than 20% inhibition on bioluminescence) during treatment and energy cost analysis (5.269 × 10−3 kWh/order/m3) in treating 10 μg/L of metoprolol containing wastewater effluent at continuous flow mode implied that the proposed BEF has a potential for wastewater treatment.