Quorum quenching, enzymatic quenching of bacterial quorum sensing, has recently proven its potential as a novel approach of biofouling control in the membrane bioreactor (MBR) for advanced wastewater treatment. However, the short catalytic lifetime and difficulty in recovering free enzyme hamper the successful application of the quorum quenching technique in the MBR under a long-term continuous operation. In this study, a magnetic enzyme carrier (MEC) was prepared by immobilizing the quorum quenching enzyme (acylase) on magnetic particles to overcome the technical limitations of free enzyme. The MEC showed no activity decrease under both continuous shaking for 14 days and 29 iterative cycles of reuse. Furthermore, the comparison of the MEC with free enzyme in a batch type MBR showed that the MEC efficiently alleviated the membrane biofouling and showed a great advantage over free enzyme in terms of recycled use and stability in mixed liquor. When the MEC was applied to the lab scale MBR in a continuous operation, it also enhanced the membrane permeability to a large extent compared with a conventional MBR with no enzyme.