Benzethonium　chloride　(BEC)　is　one　of　emerging　bacteriostatic　agents.　BEC-bearing　wastewater　generated　during　sanitary　applications　in　food　and　medication　is　easily　combined　with　other　wastewater　streams　to　flow　into　wastewater　treatment　plants.　This　study　focused　on　the　long-term　(231　days)　impacts　of　BEC　on　the　sequencing　moving　bed　biofilm　nitrification　system.　Nitrification　performance　was　tolerant　to　low　concentration　of　BEC　(≤　0.2　mg/L),　but　the　nitrite　oxidation　was　severely　inhibited　when　the　concentration　of　BEC　was　1.0–2.0　mg/L.　Partial　nitrification　maintained　about　140　days　with　nitrite　accumulation　ratio　over　80%,　mainly　caused　by　the　inhibition　of　Nitrospira,　Nitrotoga　and　Comammox.　Notably,　BEC　exposure　in　the　system　might　cause　the　co-selection　of　antibiotic　resistance　genes　(ARGs)　and　disinfectant　resistance　genes　(DRGs),　and　the　resistance　of　biofilm　system　to　BEC　was　strengthened　by　efflux　pumps　mechanism　(qacEdelta1　and　qacH)　and　antibiotic　deactivation　mechanism　(aadA,　aac(6′)-Ib　and　blaTEM).　Extracellular　polymeric　substances　secretion　and　BEC　biodegradation　were　also　contributed　to　the　system　microorganisms　resisting　BEC　exposure.　In　addition,　Klebsiella,　Enterobacter,　Citrobacter　and　Pseudomonas　were　isolated　and　identified　as　BEC　degrading　bacteria.　The　metabolites　of　N,N-dimethylbenzylamine,　N-benzylmethylamine　and　benzoic　acid　were　identified,　and　the　biodegradation　pathway　of　BEC　was　proposed.　This　study　brought　new　knowledge　about　the　fate　of　BEC　in　biological　treatment　units　and　laid　a　foundation　for　its　elimination　from　wastewater.　©　2023　Elsevier　Ltd