The intensive use of various antibiotics for clinical and agricultural purposes has resulted in their widespread use in wastewater treatment plants. However, little research has been conducted on the effects of antibiotics on nitrite accumulation, antibiotic degradation pathways, or the microbial community structure in nitrification systems. In this study, a laboratory-scale sequencing batch reactor was used to treat wastewater containing cefalexin (CFX) at different doses (5, 10, 15, and 20mg/L). The results showed that the nitrification performance was gradually inhibited with increasing CFX concentration. Ammonia-oxidizing bacteria (AOB) are more tolerant to CFX than nitrite-oxidizing bacteria (NOB). Under 15mg/L of CFX, NOB were completely suppressed, whereas AOB were partially inhibited, as evidenced by an ammonium removal efficiency of 60% and a 90% of nitrite accumulation ratio. The partial nitritation was achieved. CFX can be degraded into 2-hydroxy-3phenylpyrazine and cyclohexane through bacterial co-metabolism, and CFX degradation gradually diminishes with decreasing nitrification performance. The abundance of Nitrospira gradually decreased with increasing CFX concentration. Ferruginibacter, Hydrogenophaga, Thauera, and Pseudoxanthomonas were detected at relative abundances of 13.2%, 0.4%, 0.9%, and 1.3%, respectively, indicating their potential roles in antibiotic degradation. These findings provide insight into the interactions between antibiotics and microbial communities, which are beneficial for a better understanding of antibiotic degradation in nitrification systems. Environmental ImplicationVarious antibiotics are released to the environment, which could cause negative effects on biological nitrogen removal in wastewater treatment plants. In this study, long-term impacts of cefalexin on nitrite accumulation, antibiotic degradation and microbial community structure were investigated in a lab-scale nitrification system. The degradation products of cefalexin were quantitatively and qualitatively analyzed. The obtained results might be beneficial to achieve simultaneous antibiotic and nitrogen removal in wastewater treatment systems.