Natural and agricultural soils are important sources of nitrogen oxides (NO_x), accounting for about 10 %–20 % of the global NO_x emissions. The increased application of nitrogen (N) fertilizer in agriculture has strongly enhanced the N availability of soils in the last several decades, leading to higher soil NO_x emissions. However, the magnitude of the N fertilizer-induced soil NO_x emissions remains poorly constrained due to limited field observations, resulting in divergent estimates. Here we integrate the results from meta-analyses of field manipulation experiments, emission inventories, atmospheric chemistry modelling and terrestrial biosphere modelling to investigate these uncertainties and the associated impacts on ground-level ozone and methane. The estimated present-day global soil NO_x emissions induced by N fertilizer application vary substantially (0.84–2.2 Tg N yr⁻¹) among different approaches with different spatial patterns. Simulations with the 3-D global chemical transport model GEOS-Chem demonstrate that N fertilization enhances global surface ozone concentrations during summertime in agricultural hotspots, such as North America, western Europe and eastern and southern Asia by 0.1 to 3.3 ppbv (0.2 %–7.0 %). Our results show that such spreads in soil NO_x emissions also affect atmospheric methane concentrations, reducing the global mean by 6.7 (0.4 %) ppbv to 16.6 (0.9 %) ppbv as an indirect consequence of enhanced N fertilizer application. These results highlight the urgent need to improve the predictive understanding of soil NO_x emission responses to fertilizer N inputs and its representation in atmospheric chemistry modelling.