Understanding how agricultural management practices impact nitrous oxide (N₂O) emissions is prerequisite for developing mitigation protocols. We conducted a meta-analysis on 597 pairwise comparisons (129 papers) to assess how management affects N₂O emissions. Pairwise comparisons of practices aimed at improving fertiliser use efficiency (39%) and tillage (30%) dominated the dataset, while ecologically based nutrient management (ENM) practices constituted 15% of the pairs. In general, across management practices, the quantity of nitrogen added was a more significant driver of N₂O fluxes than was the form of nitrogen (fertiliser, legume biomass or animal manures). Manure interacted with soil texture so that in coarse soils, N₂O emissions from manures tended to be higher compared to inorganic nitrogen fertilisers. The studies of ENM strategies frequently involved over-application of nitrogen inputs in the ENM treatments. Cover crops reduced N₂O emissions compared to bare fallows. However, during the cash crop-growing season, when differences in nitrogen added and nitrogen source were confounded, the extra nitrogen inputs from cover crops were significantly correlated with the differences in N₂O emissions between treatments with and without cover crops. Overall, in 38% of the data pairs, N₂O emissions were reduced with limited impacts on yields; in half of these pairs, yields were maintained or increased while in the other half they were reduced by only ≤10%. Knowledge gaps on mitigation of agricultural N₂O emissions could be addressed by applying an ecosystem-based, cross-scale perspective in conjunction with the nitrogen saturation conceptual framework to guide research priorities and experimental designs.