Autotrophic nitrogen removal is regarded as a resource efficient process to manage nitrogen-rich residual streams. However, nitrous oxide emissions of these processes are poorly documented and strategies to mitigate emissions unknown. In this study, two sequencing batch reactors performing single-stage nitritation/anammox were operated under different aeration strategies, gradually adjusted over six months. At constant but limiting oxygen loading, synthetic reject water was fed (0.75 g-N/L · d) and high nitrogen removal efficiencies (83 ± 5 and 88 ± 2%) obtained. Dynamics of liquid phase nitrous (N2O) and nitric oxide (NO) concentrations were monitored and N2O emissions calculated. Significant decreases in N2O emissions were obtained when the frequency of aeration was increased while maintaining a constant air flow rate (from >6 to 1.7% ΔN2O/ΔTN). However, no significant effect on the emissions was noted when the duration of aeration was increased while decreasing air flow rate (10.9 ± 3.2% ΔN2O/ΔTN). The extant ammonium oxidation activity (mgNH4(+)-N/gVSS · min) positively correlated with the specific N2O production rate (mgN2O-N/gVSS · min) of the systems. Operating under conditions where anaerobic exceeds aerobic ammonium oxidation activity is proposed to minimize N2O emissions from single-stage nitritation/anammox reactors; increasing the frequency of aeration cycling is an efficient way of obtaining those conditions.