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Recently, the European Commission adopted a new strategy to halt the loss of biodiversity. Member states are expected to favor a more effective collection and redistribution of European Union (EU) funds under the current Multiannual Financial Framework for 2014–2020. Because of the large spatial variation in the distribution of biodiversity and conservation needs at the continental scale, EU instruments should ensure that countries with higher biodiversity values get more funds and resources for the conservation than other countries. Using linear regressions, we assessed the association between conservation investments and biodiversity values across member states, accounting for a variety of conservation investment indicators, taxonomic groups (including groups of plants, vertebrates, and invertebrates), and indicators of biodiversity value. In general, we found clear overall associations between conservation investments and biodiversity variables. However, some countries received more or less investment than would be expected based on biodiversity values in those countries. We also found that the extensive use of birds as unique indicators of conservation effectiveness may lead to biased decisions. Our results can inform future decisions regarding funding allocation and thus improve distribution of EU conservation funds., D.S.-F. was supported by a postdoctoral contract funded by Universidad de Castilla-La Mancha and the European Social Fund (ESF). P.A. was supported by a Ramón y Cajal contract (RYC-2011-07670) from the Spanish Ministry of Economy and Competitiveness (MINECO). This work was partly funded by the project CGL2014-56416-P (MINECO).