The synergy activity of the heterojunctions photocatalyst can be improved further by including the surface plasmon resonance of single metal atoms. For this aim, a simple calcination and hydrothermal method was used to dope single atom Co on top of the Z-type 10 wt% g-C3N4/Bi2WO6 heterojunctions which we had tested previously. The optimal Co doping was determined at 0.2 wt% Co/10 wt% g-C3N4/Bi2WO6, that it most efficiently degraded (100 mg/L) RhB under visible light irradiation (99.7% in 30 min, kinetic rate constant 0.182 min -1). This single-atom doped catalysts (Co/g-C3N4/Bi2WO6) should be most favorably used in treating practical wastewater in EC (electro-chemical)-MFC (microbial fuel cell) system. Its remarkable performance was recorded (96% COD removal and 92.8% TOC removal). The reactive oxidizing species include h+, 1O2, ·O2-, e-, and ·OH, they act together leading to the rapid degradation of pollutants. The developed Co-doped ternary catalyst has promising application prospects in pollution control in real world wastewater treatment.