In the last 30 years, the use of membrane bioreactors (MBRs) for advanced wastewater treatment and reuse have been expanded continuously, but they still suffer from excessive energy consumption resulting from the intrinsic problem of membrane biofouling. One of the major causes of biofouling in MBRs is bacterial quorum sensing (QS) via N-acylhomoserine lactones (AHLs) and/or autoinducer-2 (AI-2), enabling intra- and interspecies communications, respectively. In this study, we demonstrate that farnesol can substantially mitigate membrane biofouling in a MBR due to its quorum quenching (QQ) activity. When Candida albicans (a farnesol producing fungus) entrapping polymer beads (AEBs) were placed in the MBR, the rate of transmembrane pressure (TMP) rise-up was substantially decreased, even for lower aeration intensities. This finding corresponds to a specific aeration energy savings of approximately 40% (25% through the physical washing effect and a further 15% through the biological QQ effect of AEBs) compared to conventional MBRs without AEBs. A real-time RT-qPCR analysis revealed that farnesol secreted from C. albicans mitigated the biofilm formation in MBRs via the suppression of AI-2 QS. Successful control of biofouling and energy savings through fungal-to-bacterial QQ could be expanded to the plant scale for MBRs in wastewater treatment with economic feasibility.