Understanding of the metabolic pathways connected with a removal of micropollutant bisphenol A (BPA) may help to better design effective wastewater treatment processes. The aim of this study was to determine changes in gene expression in an aerobic granular sludge (AGS) community exposed to BPA. In the study, AGS adapted to BPA degradation was used. In this sludge, BPA was dosed; as a control sample, granules without BPA addition were used. mRNA was isolated from both samples and sequenced using the Illumina platform. Metatranscriptome analysis of AGS exposed to BPA indicated direct biodegradation as the main mechanism of BPA removal from wastewater. High expression of genes coding pilus and flagellin proteins in the BPA-exposed biomass indicated that exposition to BPA stimulated aggregation of microbial cells and formation of biofilm. In the BPA-exposed biomass, nitrogen was mainly used as an energy source, as indicated by the presence of genes coding nitrification enzymes and urease. Moreover, exposition to BPA stimulated expression of genes coding proteins responsible for xenobiotic degradation, including enzymes responsible for benzoate degradation. These results increase knowledge about BPA metabolism in complex microbial communities in wastewater treatment systems and indicate that AGS is suitable for efficiently removing BPA from wastewater.