Membrane fouling is the biggest challenge in membrane based technology operation. Studies on critical flux mainly focused on membrane bioreactor for municipal wastewater and/or greywater treatment, which can significantly differ from the ultrafiltration membrane bioreactor (UF-MBRs) to treat source separated urine. In this work, the inhibitory factors on nitrifying bacteria activity were investigated for fast acclimation of nitrifying bacteria with high ammonium concentration and optimization of a high-rate partial nitrification MBR. The maximum nitrification rate of 447 ± 50 mgN L–1 d–1 was achieved when concentration of ammonia in feed urine is approximately 4006.3 ± 225.8 mg N L–1 by maintaining desired pH around 6.2 and FA concentrations below 0.5 mgL−1. Furthermore, for the first time, the impact of different operational and filtration conditions (i.e. aeration intensity, filtration method, imposed flux, intermittent relaxation, biomass concentration) on the reversibility of membrane fouling was carried out for enhancement of membrane flux and fouling mitigation. Fouling mechanisms for minor irreversible fouling observed under sub-critical condition were pore blocking and polarization. To mitigate membrane fouling, the UF module with effective membrane surface area of 0.02 m2 is recommended to be operated at the aeration intensity of 0.4 m3 h−1, intermittent relaxation of 15 min, biomass concentration of 3.5 g L−1.