Bio-electro-Fenton powered by microbial fuel cell (MFC-powered BEF) can in-situ generate and utilize hydrogen peroxide to degrade refractory pollutants. Most of the previous works loaded transition metal on the cathode to participate in the Fenton reaction showed limited electrical or degradation performance. The coupling of alkaline-earth metal (Mg0 and MgO) and transition metal on cathode could improve the electrochemical and catalytic properties of MFC-powered BEF system, which had not been reported so far. In this research, a novel cathode of Fe–Mn–Mg/carbon fiber (Fe–Mn–Mg/CF) was developed with good polymerization effect of Mg to Fe and Mn, and outstanding production of reactive oxide species (•OH and •O2−), which further improved the overall electricity generation efficiency and enhanced the degradation of pollutants. Accordingly, the maximum power density generated in MFC-powered BEF system with Fe–Mn–Mg/CF cathode was 2.07 times higher than that of the frequently used Fe–Mn/CF. Owing to the superiority of surface holes and MgO in H+ adsorption and electron transfer, the integration of Fe, Mn with Mg promoted the in-situ generation of H2O2 and active radicals, resulting in the highest catalytic performance of degrading refractory pollutants. Initial pH, external resistance, initial concentration of contaminant and cycle use frequency of cathode were also evaluated on the degradation efficiency of the BEF system. Furthermore, reaction and degradation mechanisms were proposed from H2O2 production and free radical characterization. Overall, this study provided a novel cathode preparation approach for the MFC-powered BEF system, which vastly promoted its electrochemical and catalytic properties.