1. Despite advances in conservation efforts within Europe during recent decades, assessments highlight a need for adequate financing mechanisms to support the Natura 2000 network; the centrepiece of the EU´s Biodiversity Strategy. Besides the need for greater investment (currently only covering a fifth of the estimated cost of the network), better planning for this investment could help better achieve conservation goals. 2. We demonstrate a method that could be used to identify priority Natura 2000 sites, and species therein, that could guide investment in the future. We first used the lists of key species associated with each Natura 2000 site to map the distribution of all priority species covered by the Birds and Habitats Directives. We then used Marxan software to prioritise allocation of conservation funds among all Natura 2000 sites, while trying to mimic the observed conservation effort implemented under the LIFE Program, the main financial tool of the EU´s Biodiversity Strategy, in the period 1992-2013. 3. Some Natura 2000 sites show exceptional value, holding species that either do not, or only very rarely, occur elsewhere in the network. These priority sites were concentrated mainly on islands and in the south western, eastern and northern extremes of Europe´s mainland thus reflecting patterns in species richness and endemism. 4. We found a poor relationship between the priorities identified here and the way funds had been distributed in previous LIFE-Nature Programs. 5. Policy implications. We propose that prioritisation exercises like the one shown here could be used to inform a top-down EU regulation mechanism by providing lists of site and species priorities that better reflect European conservation needs. These recommendations, performed at continental scale, could then help guide LIFE project proposals from the Member States and fill the current gap in the coverage of priority species. This top-down control mechanism could be integrated in the current system of budget distribution, rather than replacing it completely, to enhance the efficiency of conservation investment in the EU and achievement of continental goals.18-Jan-2018