Nitrous oxide (NO) production from autotrophic nitrogen conversion processes, especially nitritation systems, can be significant, requires understanding and calls for mitigation. In this study, the rates and pathways of NO production were quantified in two lab-scale sequencing batch reactors operated with intermittent feeding and demonstrating long-term and high-rate nitritation. The resulting reactor biomass was highly enriched in ammonia-oxidizing bacteria, and converted ∼93 ± 14% of the oxidized ammonium to nitrite. The low DO set-point combined with intermittent feeding was sufficient to maintain high nitritation efficiency and high nitritation rates at 20-26 °C over a period of ∼300 days. Even at the high nitritation efficiencies, net NO production was low (∼2% of the oxidized ammonium). Net NO production rates transiently increased with a rise in pH after each feeding, suggesting a potential effect of pH on NO production. In situ application of N labeled substrates revealed nitrifier denitrification as the dominant pathway of NO production. Our study highlights operational conditions that minimize NO emission from two-stage autotrophic nitrogen removal systems.