Fluorinated quaternary ammonium-containing polymers were used as catalyst binders in microbial fuel cell (MFC) cathodes. The performance of the cathodes was examined and compared to NAFION ® and other sulfonated aromatic cathode catalyst binders using linear sweep voltammetry (LSV), impedance spectroscopy, and performance tests in single chamber air-cathode MFCs. The cathodes with quaternary ammonium functionalized fluorinated poly(arylene ether) (Q-FPAE) binders showed similar current density and charge transfer resistance (R ct) to cathodes with NAFION ® binders. Cathodes containing either of these fluorinated binders exhibited better electrochemical responses than cathodes with sulfonated or quaternary ammonium-functionalized RADEL ® poly(sulfone) (S-Radel or Q-Radel) binders. After 19 cycles (19 d), the power densities of all the MFCs declined compared to the initial cycles due to biofouling at the cathode. MFC cathodes with fluorinated polymer binders (1445 mW m -2, Q-FPAE-1.4-H; 1397 mW m -2, Q-FPAE-1.4-Cl; 1277 mW m -2, NAFION ®; and 1256 mW m -2, Q-FPAE-1.0-Cl) had better performance than those with non-fluorinated polymer binders (880 mW m -2, S-Radel; 670 mW m -2, Q-Radel). There was a 15% increase in the power density using the Q-FPAE binder with a 40% higher ion exchange capacity (Q-FPAE-1.4-H compared to Q-FPAE-1.0-Cl) after 19 cycles of operation, but there was no effect on the power production due to counter ions in the binder (Cl -vs. HCO 3 -). The highest-performance cathodes (NAFION ® and Q-FPAE binders) had the lowest charge transfer resistances (R ct) in fresh and in fouled cathodes despite the presence of thick biofilms on the surface of the electrodes. These results show that fluorinated binders may decrease the penetration of the biofilm and associated biopolymers into the cathode structure, which helps to combat MFC performance loss over time. © 2012 The Royal Society of Chemistry.