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[Display omitted] • A core–shell QQ-encapsulated structure was prepared by a standardized method. • SIPN shell enables excellent biocontainment with physical and chemical stability. • The anti-biofouling and phosphorus removal were enhanced in QQ microcapsule MBR. • QQ microcapsule promoted the application of QQ media for anti-biofouling in MBR. Microbial quorum quenching (QQ) has been proven to be a sustainable anti-biological fouling strategy for membrane bioreactors (MBR), but the long-term stability and practical application in MBR were uncertain. We reported a novel semi-interpenetrating network (SIPN) hydrogels-based design of QQ bacteria (Rhodococcus sp. BH4) encapsulation for both biofouling control and enhancement of organic pollutants removal in MBR. The microcapsule included the alginate core, chitosan thin intermediate compartment and SIPN (sodium alginate / polyacrylamide) shell, which exhibited near-perfect biocontainment, including preventing detectable QQ bacteria escape and improving mechanical strength. The QQ-microcapsules in the MBR demonstrated its significant anti-biofouling effect for treating synthetic wastewater (i.e., membrane fouling was delayed by 233%-280% compared to the control MBR membrane). Meanwhile, the efficiency of phosphorus removal was developed in QQ-microcapsule MBR because of the enhanced phosphorus removal triggered by the flocculation of polyacrylamide (PAM) fraction in SIPN. This promising QQ media brings the broad potential for biofouling control and long-term efficient operation in actual MBR wastewater treatment. [ABSTRACT FROM AUTHOR]