Microplastics (MPs) inevitably enter wastewater treatment plants (WWTPs), yet their impacts remain poorly understood. This study investigates the effects of MPs on system performance and membrane fouling in a Modified Ludzack-Ettinger (MLE)-Reciprocation Membrane Bioreactor (rMBR), an energy-efficient alternative to conventional membrane bioreactors. Additionally, the study examines changes in microbial community induced by different types and shapes of MPs—polyethylene (PE) pellets and polyester (PES) fibers— as well as biofilm formation on MPs, using next-generation sequencing. Results revealed that transmembrane pressure (TMP) increased 2–3 times faster in the presence of PE pellets, while TMP remained stable during the PES stage, implying that MP type and shape could influence biofouling behaviors. Furthermore, enhanced nitrate removal was observed in the aerobic tank due to denitrifying biofilm formation on MPs. However, PES MPs reduced nitrate removal efficiency from 99.6 ± 0.3 % to 90.9 ± 7.9 % and decreased the relative abundance of denitrifying bacteria. Numerous taxa showed affinity to PE pellets, including some pathogens, e.g., Norcadia and Mycobacterium. Notably, an uncultured phylum Candidatus Saccharibacteria dominated in membrane biofilm and MPs, reaching up to 37 % relative abundance. This study is the first to explore how different types and shapes of MPs affect membrane bioreactor systems, particularly with respect to microbial community structure and biofilm formation. The findings offer new insights into the influence of MPs on wastewater treatment processes and highlight the significance of the uncultured phylumCandidatus Saccharibacteriain membrane fouling.