Despite ambitious biodiversity policy goals, less than a fifth of the European Union's (EU) legally protected species and habitats show a favorable conservation status. The recent EU biodiversity strategy recognizes that climate change adds to the challenge of halting biodiversity loss, and that an optimal distribution of financial resources is needed. Here, we analyze recent EU biodiversity funding from a climate change perspective. We compare the allocation of funds to the distribution of both current conservation priorities (within and beyond Natura 2000) and future conservation needs at the level of NUTS-2 regions, using modeled bird distributions as indicators of conservation value. We find that funding is reasonably well aligned with current conservation efforts but poorly fit with future needs under climate change, indicating obstacles for implementing adaptation measures. We suggest revising EU biodiversity funding instruments for the 2014-2020 budget period to better account for potential climate change impacts on biodiversity. ©2014 Wiley Periodicals, Inc.