Quorum quenching (QQ) is a novel anti-biofouling strategy for membrane bioreactors (MBRs) used in wastewater treatment. However, actual operation of QQ-MBR systems for wastewater treatment needs to be systematically studied to evaluate the comprehensive effects of QQ on wastewater treatment engineering applications. In this study, a novel QQ strain, Acinetobacter pittii HITSZ001, was encapsulated and applied to a MBR system to evaluate the effects of this organism on real wastewater treatment. To verify the effectiveness of immobilized QQ beads in the MBR system, we examined the MBR effluent quality and sludge characteristics. We also measured the extracellular polymeric substances (EPS) and soluble microbial products (SMP) in the system to determine the effects of the organism on membrane biofouling inhibition. Additionally, changes in microbial communities in the system were analyzed by high-throughput sequencing. The results indicated that Acinetobacter pittii HITSZ001 is a promising strain for biofouling reduction in MBRs treating real wastewater, and that immobilization does not affect the biofouling control potential of QQ bacteria.