Few attempts have been made in previous studies to link the microbial community structure and function with nitrous oxide (N₂O) emissions at full-scale wastewater treatment plants (WWTPs). In this work, high-throughput sequencing and reverse transcriptase-qPCR (RT-qPCR) was applied to activated sludge samples from three WWTPs for two seasonal periods (winter and summer) and linked with the N₂O emissions and wastewater characteristics. The total N₂O emissions ranged from 7.2 to 937.0 g N-N₂O/day, which corresponds to an emission factor of 0.001 to 0.280% of the influent NH₄-N being emitted as N₂O. Those emissions were related to the abundance of Nitrotoga, Candidatus Microthrix and Rhodobacter genera, which were favored by higher dissolved oxygen (DO) and nitrate (NO₃⁻) concentrations in the activated sludge tanks. Furthermore, a relationship between the nirK gene expression and N₂O emissions was verified. Detected N₂O emission peaks were associated with different process events, related to aeration transition periods, that occurred during the regular operation of the plants, which could be potentially associated to increased emissions of the WWTP. The design of mitigation strategies, such as optimizing the aeration regime, is therefore important to avoid process events that lead to those N₂O emissions peaks. Furthermore, this study also demonstrates the importance of assessing the gene expression of nosZ clade II, since its high abundance in WWTPs could be an important key to reduce the N₂O emissions.