The partial nitritation/anammox (PN/A) process has been applied to ammonium-rich wastewater treatment, but the operational boundary has not been well determined for long-term stability. This pilot-scale study was targeted at a single-stage PN/A process using a sequencing batch reactor (SBR) (volume: 53 m3) and granulated activated sludge. The maximum nitrogen removal rate reached 0.83 kg N/(m3·d). Microbial analysis suggested that ammonium oxidizing bacteria were mainly present in small sludge flocs while anammox bacteria were prone to grow in large sludge granules. The PN/A performance was enhanced when dissolved oxygen (DO) was increased from 0.25 to 0.76 mg/L, and deteriorated at DO higher than 1.15 mg/L. The PN/A was inhibited at free ammonia (FA) over 77.0 mg/L. High DO or FA concentrations inhibited anammox activity and further induced high and inhibitory nitrite concentrations. Therefore, appropriate DO and FA concentrations should be controlled to achieve single-stage PN/A in SBRs.