There is increasing awareness of the presence of anticancer drugs (ACDs) in wastewater. Nonetheless, how ACDs affect the performance of wastewater treatment systems and their microbial populations remains largely unclear. This study investigated the effects of three common ACDs (cyclophosphamide, tamoxifen, and methotrexate) at varying concentrations on physicochemical parameters and drug removal efficiency in an aerobic granular sludge (AGS) system operated in a continuous-flow reactor. Additionally, it examined the abundance of active microbial communities, including nitrifiers (amoA gene from ammonia-oxidizing bacteria and archaea) and denitrifiers (napA, narG, nirK, nirS, nosZ genes), as well as the biodiversity of active prokaryotic communities. The concentration level of ACDs determines variations in biomass density, granule integrity, and removal efficiencies of organic matter (OM) and total nitrogen. Both medium and high ACD concentrations negatively impact these physicochemical parameters. The findings revealed that AGS functioning within a continuous system could help remove ACDs, but removal efficiencies depended on the specific drug and concentration applied. At medium and high ACD concentrations a marked reduction in the abundance of active bacterial and archaeal communities, including nitrifiers and denitrifiers, was observed, alongside a decline in microbial diversity and a transformation in community composition. Specific bacterial genera, which are crucial for OM degradation, nitrification and denitrification were identified as particularly sensitive to anticancer drugs. Our findings highlight the need for monitoring and managing anticancer drugs in wastewater systems, as they can substantially alter treatment performance, nitrogen-cycling communities, and bacterial community composition.