The expectations on protected areas to deliver not only biodiversity conservation but also to provide an array of different ecosystem services rise. Climate regulation and more specifically the sequestration and storage of carbon are especially seen as promising services protected areas may provide. To estimate the potential for climate-smart conservation planning in Europe, we integrate spatially explicit data on terrestrial Natura 2000 sites, soil organic carbon, and agricultural land values for the European Union. The specific objectives of this study are to analyse spatial relations between soil carbon content, land value and protected areas on European Union’s land area and to locate and quantify the proportion of land with high carbon and low economic value within and outside protected areas. We apply a unique interdisciplinary framework with methods ranging from analyses with geographical information systems, agricultural economics to statistics. Findings indicate that there is a significant overlap between Natura 2000 sites and regions with a high carbon content across Europe. Economic analyses shows that carbon-rich regions have significantly lower land values than other areas. Our results suggest that biodiversity protection and mitigation of climate change through conservation of soil carbon could be simultaneously achieved in Europe’s protected areas and beyond. We conclude that there is a notable potential for climate-smart conservation in Europe that needs to be further explored.