The ubiquitous use of antimicrobial triclocarban (TCC) has raised widespread concern about the potential impacts on wastewater treatment systems, the environment, and the human population. As important constituents of activated sludge secretions, extracellular polymeric substances (EPS) play essential roles in removing micropollutants during wastewater treatment. Here, the adsorption of TCC by sludge and EPS in a multistage biological process was investigated. The EPS was enriched upon TCC stress, and the adsorption by sludge and EPS showed multilayer heterogeneity. The adsorption constant Kf (6.3794–7.6061) of EPS was over 10 times higher than that of sludge (0.5661–0.6200) in all stages, potentially owing to the loose multilayer structure and substantial functional groups (tryptophan-protein as the main binding site) in EPS. TCC significantly inhibited the biological removal of ammonia nitrogen. Notably, TCC once reaching the cell surface, formed a stable complex with ammonia transporter (Amt, binding energy: −73.1 ± 16.6 kJ·mol−1) and bound to the selectivity filter vestibule of Amt (tryptophan 144 and serine 227), inhibiting the transport of ammonia. Our work drew molecular-level insights into the interaction between TCC and activated sludge, and evaluated the adverse impacts on treatment performance through an in silico approach, providing new information on the fate and risk of TCC in wastewater treatment systems.