Ibuprofen (IBU), a commonly used non-steroidal anti-inflammatory drug, is frequently detected in wastewater treatment systems, where it can interfere with nitrogen removal. This study investigated the effects of IBU on nitrogen removal performance and its biotransformation in a coupled sulfur autotrophic denitrification and anammox (SAD/A) system. Moreover, key parameters, such as nitrogen removal efficiency, microbial activity, community structure, and IBU degradation products, were carefully monitored. While IBU concentrations of up to 1 mg/L had negligible impacts on nitrogen removal efficiency due to the counteracting effects of slight inhibition on anammox and enhancement of sulfur autotrophic denitrification, a significant inhibition of ammonia removal occurred when the concentration increased to 10 mg/L. Quantum chemical analyses revealed that IBU underwent biotransformation through decarboxylation and hydroxylation pathways, leading to the formation of two biotransformation products with high ecological toxicity. This study is the first to elucidate the mechanisms by which IBU influences microbial communities and metabolic activities in SAD/A systems. In addition, it highlights the resilience of these systems in maintaining nitrogen removal efficiency under varying IBU concentrations, as well as the environmental risks posed by the biotransformation products of IBU.