Coagulation, magnetic ion exchange resin (MIEX) and biological activated carbon (BAC) were examined at lab scale as standalone, and sequential pre-treatments for controlling the organic fouling of a microfiltration membrane by biologically treated secondary effluent (BTSE) using a multi-cycle approach. MIEX gave slightly greater enhancement in flux than coagulation due to greater removal of high molecular weight (MW) humic substances, although it was unable to remove high MW biopolymers. BAC treatment was considerably more effective for improving the flux than coagulation or MIEX. This was due to the biodegradation of biopolymers and/or their adsorption by the biofilm, and adsorption of humic substances by the activated carbon, as indicated by size exclusion chromatography. Coagulation or MIEX followed by BAC treatment further reduced the problematic foulants and significantly improved the flux performance. The unified membrane fouling index showed that the reduction of membrane fouling by standalone BAC treatment was 42%. This improved to 65%, 70%, and 93% for alum, ferric chloride and MIEX pre-treatment, respectively, when followed by BAC treatment. This study showed the potential of sequential MIEX and BAC pre-treatment for controlling organic fouling and thus enhancing the performance of microfiltration in the reclamation of BTSE.