Emissions of the greenhouse gas nitrous oxide from the Partial Nitritation-Anammox process are of concern and can determine the carbon footprint of the process. In order to reduce nitrous oxide emissions intermittent aeration regimes have been shown to be a promising mode of operation, possibly due to an effective control of accumulation of nitrogen intermediates. However, due to frequent changes of redox conditions under intermittent aeration regimes, nitrous oxide production and emissions are dynamic. In this study the production and emission dynamics of nitrous oxide in an intermittently aerated sequencing batch reactor were monitored in high temporal resolution, the contribution of different redox conditions to overall nitrous oxide production was quantified and the most relevant factors for nitrous oxide production were identified. The average fraction of nitrous oxide produced (per unit ammonium removed) was 1.1 ± 0.5%. Cycle-averaged approx. 80% of nitrous oxide was produced during aerated phases, the remaining 20% were produced during non-aerated phases. Yet, the intra-cycle dynamics of nitrous oxide were substantial. The net-production rate of nitrous oxide during aerated phases correlated with the ammonia removal rate, whereas the concentration of nitrite determined the production during non-aerated phases. While aerated phases contributed predominantly at the beginning of reactor cycles, non-aerated phases became the dominant source of nitrous oxide at the end. Particularly low net-production rates were observed at ammonia removal rates below 5 mg NH3-N*gVSS−1*L−1, when the fraction of nitrous oxide produced was 0.011 ± 0.004% (per ammonia removed). Based on the nitrous oxide dynamics and correlations, reactor operation at relatively low nitrogen loadings (below 100 mg NH4+-N*L−1), ammonia removal rates of approx. 5 mg NH3-N*gVSS−1*L−1 and nitrite concentrations below 1 mg NO2−1-N*L−1 appears as beneficial for low emission of nitrous oxide.