In this study, short-term experiments were conducted with different configurations of membrane hybrid systems to treat biological treated sewage effluent containing refractory organic pollutants: (i) submerged hollow fiber microfiltration (SMF) alone; (ii) spiral flocculator (SF)-SMF without settling; (iii) SF-PAC-SMF without settling and (iv) SMF with magnetic ion exchange resin MIEXw pretreatment. The results indicated that the pre-flocculation of SF could improve the mitigation of membrane fouling significantly even when the system was operated at a high membrane filtration rate. The transmembrane pressure (TMP) of SF-PAC-SMF only increased marginally (0.8 kPa over 8 hours). SF-SMF without the addition of powdered activated carbon (PAC) also took a relatively long duration for the TMP to increase. The TMP only increased by 2.5 kPa over 8 hours. The SF-PAC-MF system resulted in a high dissolved organic carbon (DOC) removal of more than 96%. When used as pre-treatment to submerged membranes, the fluidized bed MIEXw contactor could remove a significant amount of organic matter in wastewater. This pre-treatment helped to reduce the membrane fouling and kept the TMP low during the membrane operation.