This study shows the start-up and operation of a full-scale sequencing batch reactor (SBR) with a volume of 550 m³ for deammonification of reject water from sludge dewatering over the first 650 days of operation. The SBR was operated with discontinuous aeration and achieved an optimum of around 85% of ammonium removal at a load of 0.17 kg m⁻³ d⁻¹. The application of batch tests for the activity measurement of aerobic ammonium and nitrite oxidizing bacteria and anaerobic ammonium oxidizing bacteria were proven to support the identification of setbacks in reactor operation. Furthermore, the calculation of the oxygen uptake rates from online oxygen measurements helped to explain the overall reactor performance. The aeration regime is a key parameter for stable operation of such an SBR for deammonification. At aeration/non-aeration time ranges from 6-9 min, the best results with respect to turnover rates and low nitrate production were achieved. Compared with the nitrification/denitrification SBR operated in parallel with methanol as the carbon source, a significant reduction in costs for energy and chemicals was achieved. The costs for maintenance slightly increased.