In this study, the effect of a high concentration of powdered activated carbon (PAC) on pollutant removal and microbial communities was systematically investigated. Micropollutant removal by the ‘control’ MBR (without PAC addition) was pollutant-specific and was mainly controlled by their molecular properties. The PAC-MBR achieved enhanced removal of micropollutant by 10% (ofloxacin) to 40% (caffeine). Analysis of the microbial communities in the sludge samples collected from both MBRs indicated an increase in the abundance of 24 (out of 31) genera following PAC addition. Notably, bacterial diversity enriched, particularly in the anoxic zone of the PAC-MBR, indicating a positive impact of recirculating mixed liquor containing PAC from the aerobic to the anoxic zone. In addition, PAC improved the abundance of Comamonas and Methanomethylovorans (up to 2.5%) that can degrade recalcitrant micropollutants. According to the quantitative PCR (qPCR) analysis, the copies of functional genes (nirS, nosZ and narG) increased in PAC-MBR. This study demonstrated that MBR could be operated at a high PAC concentration without compromising the pollutant removal and microbial community evolution during wastewater treatment.