Fenton-based microbial fuel cells offer an innovative approach to tertiary wastewater treatment by integrating bioelectrochemical systems with advanced oxidation processes. This hybrid technology can overcome the limitations of conventional tertiary treatment by coupling microbial degradation at the anode with Fenton-driven oxidation at the cathode. The Fenton-microbial fuel cells can achieve a higher contaminant removal efficiency while simultaneously generating electricity. Further, the Fenton-microbial fuel cells can lower operational costs due to in situ H2O2 production and higher pollutant degradation rate. Moreover, the anodic microbial degradation can achieve chemical oxygen demand reduction efficiencies exceeding 90% in both synthetic and real wastewater matrices. This chapter explores the key principles, design factors, and performance aspects of Fenton-based microbial fuel cells. It also discusses their future potential as an eco-friendly solution for integrating wastewater treatment and energy recovery in wastewater management.