We conduct the first 4D-Var inversion of NH 3 accounting for NH 3 bi-directional flux, using CrIS satellite NH 3 observations over Europe in 2016. We find posterior NH 3 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 NH 3 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 NH 3 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 NH 3 emissions from both schemes generally improve the magnitude and seasonality of simulated surface NH 3 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 NH 3 . This contrast highlights the need for accurately simulating diurnal variability of NH 3 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 NH 3 emissions estimates associated with treatment of NH 3 surface exchange.Plain Language Summary Atmospheric ammonia contributes to air pollutants and excessive deposition of reactive nitrogen that is detrimental to sensitive ecosystems. Ammonia is emitted mainly by agricultural livestock and fertilizer use. While surface measurements of NH 3 are sparse, satellite observations can provide near daily global coverage. Here we calculate monthly NH 3 emissions over Europe, the only region adopting NH 3 control policies, using an air quality model coupled with a process-based bi-directional NH 3 flux scheme and NH 3 measurements observed by the CrIS satellite instrument. Our CrIS-derived annual regional total anthropogenic NH 3 emissions are close (<2% difference) to statistic-based bottom-up estimates and are 10%-20% lower than when treating NH 3 exchange between the atmosphere and biosphere as one-way CAO ET AL.