Oxygen reduction reaction (ORR) provides a vital role for microbial fuel cells (MFCs) due to its slow reaction kinetics compared with the anodic oxidation reaction. How to develop new materials with low cost, high efficacy, and eco-friendliness which could replace platinum-based electrocatalysis is a challenge that we have to resolve. In this work, we accomplished this successfully by means of a facile strategy to synthesize a metallic organic framework-derived Fe, N, S co-doped carbon with FeS as the main phase. The Fe/[email protected]/C-0.5 catalyst demonstrated outstandingly enhanced ORR activity in neutral PBS and alkaline media, compared to that of commercial 20% Pt-C catalyst. Here, we started-up and operated two parallel single-chamber microbial fuel cells of an air cathode, and those cathode catalysts were Fe/[email protected]/C-0.5 and commercial Pt-C (20% Pt), respectively. Scanning electron microscopy (SEM) elaborated that the Fe/[email protected]/C-0.5 composite did not change the polyhedron morphology of ZIF-8. According to X-ray diffractometry(XRD) curves, the main crystal phase of the resulted Fe/[email protected]/C-0.5 was FeS. The chemical environment of N, S, and Fe which are anticipated to be the high-efficiency active sites of ORR for MFCs were investigated by X-ray photoelectron spectroscopic(XPS). Nitrogen adsorption/desorption techniques were used to calculate the pore diameter distribution. In brief, the obtained Fe/[email protected]/C-0.5 material exhibited a pronounced reduction potential at 0.861 V (versus Reversible Hydrogen Electrode(RHE)) in 0.1M KOH solution and −0.03 V (vs. SCE) in the PBS solution, which both outperform the benchmark platinum-based catalysts. Fe/[email protected]/C-0.5-MFC had a higher Open Circuit Voltage(OCV) (0.71 V), stronger maximum power density (1196 mW/m2), and larger output voltage (0.47 V) than the Pt/C-MFC under the same conditions.