Climate and land use changes are major threats to biodiversity. To preserve biodiversity, networks of protected areas have been established worldwide, like the Natura 2000 network across the European Union (EU). Currently, this reserve network consists of more than 26000 sites covering more than 17% of EU terrestrial territory. Its efficiency to mitigate the detrimental effects of land use and climate change remains an open research question. Here, we examined the potential current and future geographical ranges of four birds of prey under scenarios of both land use and climate changes. By using graph theory, we examined how the current Natura 2000 network will perform in regard to the conservation of these species. This approach determines the importance of a site in regard to the total network and its connectivity. We found that sites becoming unsuitable due to climate change are not a random sample of the network, but are less connected and contribute less to the overall connectivity than the average site and thus their loss does not disrupt the full network. Hence, the connectivity of the remaining network changed only slightly from present day conditions. Our findings highlight the need to establish species-specific management plans with flexible conservation strategies ensuring protection under potential future range expansions. Aquila pomarina is predicted to disappear from the southern part of its range and to become restricted to northeastern Europe. Gyps fulvus, Aquila chrysaetos, and Neophron percnopterus are predicted to locally lose some suitable sites; hence, some isolated small populations may become extinct. However, their geographical range and metapopulation structure will remain relatively unaffected throughout Europe. These species would benefit more from an improved habitat quality and management of the existing network of protected areas than from increased connectivity or assisted migration.