Ammonia-oxidizing　archaea　(AOA)　are　promising　candidates　for　replacing　ammonia-oxidizing　bacteria　in　wastewater　treatment.　However,　limited　efforts　have　been　made　to　enrich　copiotrophic-AOA　in　situ　competitively.　To　this　end,　two　laboratory-scale　intermittent　aerated　biofilters　(upflow-aerated　biofilter　(R1)　and　downflow-aerated　biofilter　(R2))　were　comparatively　employed　for　the　treatment　of　mainstream　wastewater.　An　extended　non-aerobic　cycling　strategy　led　to　higher　residual　ammonia-nitrogen　levels　(0.01–18.7　mg/L),　denser　biofilms,　and　facilitated　the　dominance　of　Nitrosocosmicus-like　AOA　(R1:　70.31　%;　R2:　82.32　%).　Additionally,　the　AOA　in　both　biofilters　were　the　main　contributors　(62　%–66　%)　to　the　highly　efficient　nitrification　process.　Compared　with　R1,　R2　had　a　higher　abundance　of　Nitrosomonas　and　Nitrospira,　a　lower　ammonia　oxidation　rate,　and　a　simpler　co-occurrence　network　of　nitrifiers.　The　protein　content　induced　by　intermittent　aeration　significantly　affected　the　AOA　community.　Candidatus　Brocadia　(3.62　%–7.82　%)　was　also　auto-enriched　in　both　biofilters.　Therefore,　in　situ　enrichment　of　Nitrosocosmicus-dominant　nitrifying　microorganisms　is　conducive　to　developing　an　environment-friendly,　energy-efficient,　high　ammonia-nitrogen　removal　AOA-based　partial　nitrification-anammox　process.　©　2025　Elsevier　Inc.