System of a microbial fuel cell (MFC) and a catalytic oxidation reactor (COR) was developed. In the MFC-COR system, H2O2 generated at the MFC cathode and residual dissolved oxygen could both be used as oxidants for Congo red degradation in the presence of iron phthalocyanine-based catalyst. Over 90% of Congo red was degraded within 72 h in neutral solution. The open-circuit potential and maximum power density of the MFC reactor were measured as 0.615 V and 808.3 mW/m3, respectively. The iron phthalocyanine-based catalyst was still active enough even after 33 cycles of operation. LC–MS analysis showed that Congo red was decomposed into less toxic and more biodegradable organics including malonic acid and maleic acid. This MFC-COR system can be a promising alternative for simultaneously biodegradable and refractory pollutant removal.