Large differences between the water and air pressure in microbial fuel cells (MFCs) can deform and damage cathodes. To avoid deformation, the cathode air pressure was controlled to balance pressure differences between the air and water. Raising the air pressures from 0 to 10 kPa at a set cathode potential of −0.3 V (versus Ag/AgCl) enhanced cathode performance by 17%, but pressures ≥25 kPa decreased current and resulted in air leakage into the solution. Matching the air pressure with the water pressure avoided cathode deformation and improved performance. The maximum power density increased by 15%, from 1070 ± 20 to 1230 ± 70 mW m, with balanced air and water pressures of 10–25 kPa. Oxygen partial pressures ≥12.5 kPa in the cathode compartment maintained the oxygen reduction rate to be within 92 ± 1% of that in ambient air. The use of pressurized air flow through the cathode compartments can enable closer spacing of the cathodes compared to passive gas transfer systems, which could make the reactor design more compact. The energy cost of pressurizing the cathodes was estimated to be smaller than the increase in power that resulted from the use of pressurized cathodes.