Issues associated with accumulating microplastic (MP) in sewage sludge during wastewater treatment in a membrane bioreactor (MBR) system have not been studied in detail. Here, we investigated the microplastic’s effects on floc characteristics, microbial community compositions, and fouling behavior inside sequencing-batch MBRs. MBRs were operated with 0, 7, 15, and 75 MPs/L of feed for 124-days. Results indicated that MP presence decreased sludge floc size, floc hydrophobicity, and extracellular polymeric substance (EPS) molecular size, and increased EPS concentration and the floc’s negative zeta potential. These results were attributed to the facilitation of divalent cation (Ca²⁺ and Mg²⁺) uptake by MPs that weakened ion-bridging interactions within the sludge flocs. MPs accumulation slightly affected microbial structure and diversity. Relative abundances of dominant phyla, Actinobacteria, also decreased substantially. MPs also acted like a scouring material on membrane surfaces, inducing transformation of matured biofilm structures where protein content was substantially lower than nucleic acid content, in contrast to the control. Overall, MPs’ negative effects on sludge flocs were counteracted by their scouring effect; consequently, SB-MBRs operated up to 4 months did not suffer from severe cake fouling, compared to control.