Two laboratory-scale single-stage submerged membrane bioreactors (MBRs) were operated in parallel to examine the effect of different flux conditions and several fouling mitigation methods. After control operation (filtration only), three fouling control methods (relaxation, standard backwash and chemical backwash) at 27 LMH flux and four different flux conditions (54, 36, 27 and 18 LMH) with standard backwash were applied. Physical performance of MBRs was evaluated based on the operational duration to reach maximum transmembrane pressure and the volume of permeate produced during the operational duration. Then relative cost–benefit analysis was carried out. Results showed that the combination of chemical backwash and standard backwash was the most effective for fouling mitigation in terms of physical improvement of MBR performance. However, the combination proved less economical (400% + α relative cost) than standard backwash alone (343% relative cost), because of the additional cost for pumps and chemical. It also showed that lower flux (18 LMH) is desirable as it showed better physical performance (1,770% improvement as compared to the highest flux, 54 LMH) and proved more economical than higher flux configuration. Therefore, it is concluded that the operation with standard backwash at the lowest possible flux is the best combination to improve MBR performance as well as long-term cost–benefit.