The northern Indian Ocean is a hotspot of nitrous oxide (N2O) emission to the atmosphere. Yet, the direct link between production and emission of N2O in this region is still poorly constrained, in particular the relative contributions of denitrification, nitrification and ocean transport to the N2O efflux. Here, we implemented a mechanistically-based N2O cycling module into a regional ocean model of the Indian Ocean to examine how the biological production and transport of N2O control the spatial variation of N2O emissions in the basin. The model captures the upper ocean physical and biogeochemical dynamics of the northern Indian Ocean, including vertical and horizontal N2O distribution observed in-situ and regionally integrated N2O emissions of 286\(\pm\)152 Gg N yr−1 (annual mean\(\pm\)seasonal range) in the lower range of the observation-based reconstruction (391\(\pm\)237 Gg N yr−1). N2O emissions are primarily fueled by nitrification in or right below the surface mixed layer (∼57%, including 26% in the mixed layer and 31% right below), followed by denitrification in the oxygen minimum zones (~30%) and N2O produced elsewhere and transported into the region (~13%). Overall, ∼74% of the emitted N2O is produced in subsurface and transported to the surface in regions of coastal upwelling, winter convection or turbulent mixing. This spatial decoupling between N2O production and emissions underscores the need to consider not only changes in environmental factors critical to N2O production (oxygen, primary productivity etc.) but also shifts in ocean circulation that control emissions when evaluating future changes in global oceanic N2O emissions.