Nitrous oxide (N2O) emissions from wastewater treatment are getting increased attention because their global warming potential is around 300 times that of carbon dioxide. The aim of the study was to measure nitrous oxide emissions from one stage partial nitrification/anammox (Anaerobic Ammonium Oxidation) reactors, where nitrogen is removed in a biological way. The first part of the experimental study was focused on the measurements of nitrous oxide emissions from two pilot scale reactors in the long term; one reactor with intermittent aeration at 25 °C and the other reactor with continuous aeration at 22–23 °C. The second part of the experiment was done to evaluate the influence of different nitrogen loads and aeration strategies, described by the ratio between the non-aerated and aerated phase and the dissolved oxygen concentrations, on nitrous oxide emissions from the process. The study showed that 0.4–2% of the nitrogen load was converted into nitrous oxide from two reactors. With higher nitrogen load, the amount of nitrous oxide emission was also higher. A larger fraction of nitrous oxide was emitted to the gas phase while less was emitted with the liquid effluent. It was also found that nitrous oxide emissions were similar under intermittent and continuous aeration.