AbstractWe conduct the first 4D‐Var inversion of NH₃ accounting for NH₃ bi‐directional flux, using CrIS satellite NH₃ observations over Europe in 2016. We find posterior NH₃ emissions peak more in springtime than prior emissions at continental to national scales, and annually they are generally smaller than the prior emissions over central Europe, but larger over most of the rest of Europe. Annual posterior anthropogenic NH₃ emissions for 25 European Union members (EU25) are 25% higher than the prior emissions and very close (<2% difference) to other inventories. Our posterior annual anthropogenic emissions for EU25, the UK, the Netherlands, and Switzerland are generally 10%–20% smaller than when treating NH₃ fluxes as uni‐directional emissions, while the monthly regional difference can be up to 34% (Switzerland in July). Compared to monthly mean in‐situ observations, our posterior NH₃ emissions from both schemes generally improve the magnitude and seasonality of simulated surface NH₃ and bulk NH_x wet deposition throughout most of Europe, whereas evaluation against hourly measurements at a background site shows the bi‐directional scheme better captures observed diurnal variability of surface NH₃. This contrast highlights the need for accurately simulating diurnal variability of NH₃ in assimilation of sun‐synchronous observations and also the potential value of future geostationary satellite observations. Overall, our top‐down ammonia emissions can help to examine the effectiveness of air pollution control policies to facilitate future air pollution management, as well as helping us understand the uncertainty in top‐down NH₃ emissions estimates associated with treatment of NH₃ surface exchange.