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The potent greenhouse gas nitrous oxide (N₂O) originates primarily from natural and engineered microbiomes. Emission seasonality is widely reported while the underlying metabolic controls remain largely unresolved, hindering effective mitigation. We use biological wastewater treatment as tractable model ecosystem over nearly two years. Long-term metagenomic-resolved metaproteomics is combined with ex situ kinetic and full-scale operational characterization. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving N₂O emissions is resolved. We explain the dynamics in nitrite accumulation with the kinetic unbalance between ammonia and nitrite oxidisers, and identify nitrifier denitrification as the prime N₂O-producing pathway. The dissolved O₂ emerged as the key actionable parameter for emission control. This work exemplifies the yet-to-be-realized potential of multi-meta-omics approaches for the mechanistic understanding and ecological engineering of microbiomes, ultimately advancing sustainable biotechnological developments.