Reducing surface ozone to meet the European Union’s target for human health has proven challenging despite stringent controls on ozone precursor emissions over recent decades. The most extreme ozone pollution episodes are linked to heatwaves and droughts, which are increasing in frequency and intensity over Europe, with severe impacts on natural and human systems. Here, we use observations and Earth system model simulations for the period 1960–2018 to show that ecosystem–atmosphere interactions, especially reduced ozone removal by water-stressed vegetation, exacerbate ozone air pollution over Europe. These vegetation feedbacks worsen peak ozone episodes during European mega-droughts, such as the 2003 event, offsetting much of the air quality improvements gained from regional emissions controls. As the frequency of hot and dry summers is expected to increase over the coming decades, this climate penalty could be severe and therefore needs to be considered when designing clean air policy in the European Union.