The long-term exposure of cerium oxide nanoparticles (CeO2 NPs) at 5, 20, and 50 mg/L to the biofilm and its impact on the treatment of synthetic wastewater, containing phenol, in a trickling bioreactor (TBR) were examined. An increase of 38.1 % in the reactive oxygen species (ROS) production and 29.0 % in the lactate dehydrogenase (LDH) release indicated that CeO2 NPs were toxic to the microorganisms at 50 mg/L and disrupted the integrity of the microbial membrane within the community. Phenol biodegradation, total nitrogen (TN), and total phosphorus (TP) removal slightly changed from 98.6, 53.7, and 13.0 % in the absence of NPs to respectively 96.5, 49.7, and 9.0 % in the presence of 50 mg/L CeO2 NPs. High-throughput sequencing after prolonged 30-day exposure to CeO2 NPs showed that the microbial community could self-regulate the population by adjusting species composition in response to the presence of NPs. The relative abundance of some sensitive species such as Castellaniella defragrans declined from 39.5 to 0.6 % in the presence of NPs. However, other species such as Comamonadaceae bacterium thrived and became more prevalent. The TBR effectively removed phenol, TN, and TP in the presence of CeO2 NPs, benefiting from the cells immobilization that limited the access of NPs to the deep layers of biofilm.