Recently, interspecies quorum quenching by bacterial cells encapsulated in a vessel was described and shown to be efficient and economically feasible for biofouling control in membrane bioreactors (MBRs). In this study, free-moving beads entrapped with quorum quenching bacteria were applied to the inhibition of biofouling in a MBR. Cell entrapping beads (CEBs) with a porous microstructure were prepared by entrapping quorum quenching bacteria ( Rhodococcus sp. BH4) into alginate beads. In MBRs provided with CEBs, the time to reach a transmembrane pressure (TMP) of 70 kPa was 10 times longer than without CEBs. The mitigation of biofouling was attributed to both physical (friction) and biological (quorum quenching) effects of CEBs, the latter being much more important. Because of the quorum quenching effect of CEBs, microbial cells in the biofilm generated fewer extracellular polymeric substances and thus formed a loosely bound biofilm, which enabled it to slough off from the membrane surface more easily. Furthermore, collisions between the moving CEBs and membranes gave rise to frictional forces that facilitated detachment of the biofilm from the membrane surface. CEBs bring bacterial quorum quenching closer to being a practical solution to the problem of biofouling in MBRs.