A continuous, on-line quantification of the nitrous oxide (N₂O) emissions from a full-scale sequencing batch reactor (SBR) placed in a municipal wastewater treatment plant (WWTP) was performed in this study. In general, N₂O emissions from the biological wastewater treatment system were 97.1 ± 6.9 g N₂O–N/Kg₄NH⁺−N consumed or 6.8% of the influent ₄NH⁺−N load. In the WWTP of this study, N₂O emissions accounted for over 60% of the total carbon footprint of the facility, on average. Different cycle configurations were implemented in the SBR aiming at reaching acceptable effluent values. Each cycle configuration consisted of sequences of aerated and non-aerated phases of different time length being controlled by the ammonium set-point fixed. Cycles with long aerated phases showed the largest N₂O emissions, with the consequent increase in carbon footprint. Cycle configurations with intermittent aeration (aerated phases up to 20–30 min followed by short anoxic phases) were proven to effectively reduce N₂O emissions, without compromising nitrification performance or increasing electricity consumption. This is the first study in which a successful operational strategy for N₂O mitigation is identified at full-scale.