Display omitted •A high NRE of 70% was obtained by a PNA-AICB with 50 mg-NH4/L influent.•Control of DO and aeration rate were the key factors for the stable operation.•A long time was needed for performance recovery via aeration adjustment.•Candidatus Brocadia and Nitrosomonas were dominant after the recovery.•Activated AOB, dominated AMX, suppressed NOB & controlled HB were vitally important. A one-stage airlift internal circulation biofilm reactor was continuously operated for 668 days to treat 50 mg/L of ammonia wastewater to pursue the long-term stability of partial nitritation and anammox (PNA) process. The operational performance and microbial community structure of the biofilm and the flocs were investigated. A nitrogen removal efficiency (NRE) of 70% was obtained successfully at a dissolved oxygen (DO) of 0.05–0.15 mg/L by regulating aeration rate. The microbial analysis indicated Candidatus Brocadia (29.5%) and Nitrosomonas (6.8%) were dominant in both biofilms and flocs. It was found that DO control and aeration rate were the key factors in performance stability, and a stable performance could be recovered and maintained under oxygen-limiting conditions. Further, the achievement of activated ammonia oxidation bacteria (AOB), dominated anammox bacteria (AMX), suppressed NOB, and controlled heterotrophic bacteria (HB) in the biofilms played a major role in the long-term stable operation.