To be able to fulfill the Paris agreement regarding anthropogenic greenhouse gases, all potential emissions must be mitigated. Wastewater treatment plants should aim to eliminate emissions of the most potent greenhouse gas, nitrous oxide (N2O). In this study, these emissions were measured at a full-scale reject water treatment tank during two different operation modes: nitrification/denitrification (N/DN) operating as a sequencing batch reactor (SBR), and deammonification (nitritation/anammox) as a moving bed biofilm reactor (MBBR). The treatment process emitted significantly less nitrous oxide in deammonification mode 0.14–0.7%, compared to 10% of total nitrogen in N/DN mode. The decrease can be linked to the changed feeding strategy, the lower concentrations of nitrite, a lower load of ammonia oxidized, a shorter aeration time, the absence of non-optimized ethanol dosage or periodic lack of oxygen as well as the introduction of biofilm. Further, evaluation was done how the operational pH set point influenced the emissions in deammonification mode. Lower concentrations of nitrous oxide were measured in water phase at higher pH (7.5–7.6) than at lower pH (6.6–7.1). This is believed to be mainly because of the lower aeration ratio and increased complete denitrification at the higher pH set point.