<p>Biological nitrogen removal is a main contributor to the carbon footprint of municipal wastewater treatment plants (MWWTPs). Anaerobic ammonium oxidation (anammox) is key to decarbonizing MWWTPs. However, anammox technology has long been developed following the ‘hotspot’ concept, which spatially confines anammox to specific zones in MWWTPs, leaving its potential underexploited in mainstream treatment. Here we propose a ‘multi-zonal anammox’ concept to expand the anammox process throughout the whole MWWTP mainstream. It allows the implementation of anammox in existing MWWTPs with minimal reconstruction requirements. We evaluated the feasibility of this concept in an anaerobic–anoxic–oxic (A²O) biosystem, which is one of the most widely used processes in MWWTPs. During a 2-year-long operation, anammox bacteria highly self-enriched and contributed to nitrogen removal throughout the mainstream, with relative abundances reaching 4.8%, 5.7–10.0% and 0.2–1.0% in anaerobic, anoxic and oxic zones, respectively. The multi-zonal anammox enhanced nitrogen removal efficiency by 20%, reduced aerating electricity input by 20%, mitigated nitrous oxide emissions by 66% and eliminated the need for supplemental organic carbon. Overall, this work opens a promising avenue for implementing the anammox process, paving the way towards sustainable wastewater management.</p>