Microbial fuel cells (MFCs) are a novel technique for converting biodegradable materials into electricity. In this study, the efficiency of mixed crystal (TiO2:ZnO) as a membrane modifier of a low-cost, antifouling and self-cleaning cation exchange membrane for MFCs was studied. The modification was prepared using polydopamine (PDA) as the bio-inspired glue, followed by gravity deposition of a mixture of catalyst nanoparticles (TiO2:ZnO 0.03%, 1:1 ratio) as anti-biofouling agents. The effects of the membrane modification were evaluated in terms of power density, open circuit potential, coulombic efficiency, anti-biofouling properties and also color and COD removal efficiency. The results showed that the use of the PDA-modified membrane and a mixture of catalysts facilitated the transfer of cations released during the oxidation process in the anodic compartment of the MFC, which increased the power generation in the MFC by 2.5 times and 5.7 times the current compared to pristine and PDA pristine membranes, decreased the MFC operating cycle time from 5 to 3 days, doubled the lifetime of the membranes and demonstrated higher COD removal efficiency and color removal. Finally, SEM and AFM analysis showed that the modification significantly minimized surface fouling. The modified membranes in this study proved to be a potential alternative to the expensive membranes currently used in MFCs, furthermore, this modification could be an interesting alternative modification for other potential membranes for use in MFCs, due to the fact that the catalyst activation was only performed with visible light (artificial and solar), which could decrease operating costs.