Membrane fouling is a major challenge in membrane bioreactors (MBRs) for wastewater treatment. This study investigates the effects of disturbance and solid retention time (SRT) on quorum-quenching (QQ) MBRs relative to antifouling efficacy and microbial community change. The fouling rate increases with the applied disturbance at a short SRT, counteracting the antifouling effect of QQ; however, it decreases with QQ at a long SRT. The microbial community appears to be responsible for such MBR behaviors. Several bacterial species belonging to the biofilm-forming group are dominant after disturbance, resulting in substantive membrane fouling. However, the balance between the bacterial species plays a key role in MBR fouling propensity when stabilized. Koflera flava becomes dominant with QQ, leading to reduced membrane fouling. QQ makes the MBR microbial community more diverse, while lowering its richness. QQ with long SRT would be a favorable operational strategy for effective MBR fouling control.