© 2016 The Authors. Air cathode microbial fuel cells (MFCs) were used in a cascade-system, to treat neat human urine as the fuel. Their long-term operation caused biodeterioration and biofouling of the cathodes. The cathodes were made from two graphite-painted layers, separated by a current collector. The initial performance of the MFCs was reaching average values of 105.5 ± 32.2 μW and current of 1164.5 ± 120.2 μA. After 3 months of operation the power performance decreased to 9.8 ± 3.5 μW, whilst current decreased to 461.2 ± 137.5 μA. Polarisation studies revealed significant transport losses accompanied by a biofilm formation on the cathodes. The alkaline lysis procedure was established to remove the biomass and chemical compounds adsorb...