Nitrous oxide (N2O) is a greenhouse gas with a significant global warming potential. A dynamic model was developed to estimate the N2O pro- duction and emission in a full-scale sequencing batch reactor (SBR) municipal wastewater treatment plant (WWTP). Based on the Activated Sludge Model 1 (ASM1), the model considered all known biological and abiotic N2O production pathways along with the application of a ‘stripping effectivity’ (SE) coefficient for reflecting the non-ideality of the stripping model. N2O data of two different cycles (types B and C) were used for the model calibration. Cycle B involved the alternation amongst aerated and non-aerated phases, whereas cycle C included a unique long aerobic phase. Optimizing the dissolved oxygen (DO) and SE parameters for both cycles provided a good fit of the model (DO = 1.6 mg L−1 and SE = 0.11 for cycle B, and DO = 1.66 mg L−1 and SE = 0.11 for cycle C). In both cases, N2O emission peaks were related to high nitrite concentration in the liquid phase. Nitrifier denitrification was identified as the predominant biological pathway for N2O generation. Although SBR oper- ation occurred at similar DO and SE values for both cycles, the emission factor was significantly different; 0.8% for cycle B and 1.5% for cycle C, indicating the impact of cycle configuration on the N2O emission. Thus, optimized SBR operation is essential in order to achieve a low overall carbon footprint through the avoidance of high N2O emissions and energy requirements.