In the European Union (EU) efforts to conserve biodiversity have been consistently directed towards the protection of habitats and species through the designation of protected areas under the Habitats Directive (92/43/ECC). These biodiversity conservation efforts also have the potential to maintain or improve the supply of ecosystem services; however, this potential has been poorly explored across Europe. This paper reports on a spatial assessment of the relationships between biodiversity, ecosystem services, and conservation status of protected habitats at European scale. We mapped at 10 km resolution ten spatial proxies for ecosystem service supply (four provisioning services, five regulating services and one cultural service) and three proxies for biodiversity (Mean Species Abundance, tree species diversity and the relative area of Natura 2000 sites). Indicators for biodiversity and aggregated ecosystem service supply were positively related but this relationship was influenced by the spatial trade-offs among ecosystem services, in particular between crop production and regulating ecosystem services. Using multinomial logistic regression models we demonstrated that habitats in a favourable conservation status provided more biodiversity and had a higher potential to supply, in particular, regulating and cultural ecosystem services than habitats in an unfavourable conservation status. This information is of utmost importance in identifying regions in which measures are likely to result in cost-effective progress towards both new biodiversity conservation and ecosystem services targets adopted by the Convention on Biological Diversity (CBD) and the EU Biodiversity Strategy to 2020.