This study compared the performance between membrane-coupled moving bed biofilm reactor (M-MBBR) and a conventional membrane bioreactor (MBR) in parallel. Extensive tests were conducted in three pilot-scale experimental units over 6 months. Emphasis was placed on the factors that would affect the performance of membrane filtration. The results showed that the concentrations of soluble microbial product (SMP), colloidal total organic carbon and transparent exopolymer particles in the M-MBBR systems were not significantly different from those in the control MBR system. However, the fouling rates were much higher in the M-MBBR systems as compared to the conventional MBR systems. This indicates membrane fouling potential was related not only to the concentration of SMP, but also to their sources and characteristics. The addition of polyaluminum chloride could reduce the fouling rate of the moving bed biofilm reactor unit by 56.4–84.5% at various membrane fluxes.