The coronavirus outbreak in 2020 had devastating impact on human life, albeit a positive effect for the environment reducing primary atmospheric constituents and improving air quality. Here we present for the first-time inverse modelling estimates of ammonia emissions during the European lockdowns based on satellite observations. Ammonia that originates mainly from agriculture is not projected to be strongly influenced by restrictions, as practically agricultural activity never ceased. The key result is a -1.5% decrease in emissions in the first half of 2020 compared to the same period in 2016–2019 attributed to changes in ammonia’s atmospheric levels and an abrupt − 11.7% decrease due to reductions in the traffic-related precursors of atmospheric acids, with which ammonia reacts to form secondary aerosols. The same was found when comparing emissions before, during and after lockdowns, namely a -1.2% and − 13.5% decrease, and a rebound of + 5.9% when restrictions were relaxed. Despite the drop in emissions, satellite levels of ammonia increased. On one hand, this was due to the reduction of atmospheric acids that caused binding less ammonia; on the other, the reduction of traffic emissions in Europe increased the oxidative capacity of the atmosphere resulting in nitrate abatement that favored accumulation of free ammonia.