Many of Europe’s unique habitats are highly threatened. In order to tackle these threats, the European Union (EU) is annually financing, mainly through its LIFE programme, conservation actions aimed at improving the conservation status of its habitats. We analysed the allocation of the programme’s budget since its inception in 1992 and we found that the number of projects implemented within the EU member states is only weakly related to the number of habitats within them (R2 = 0.39). In some states, fewer than 25% of the habitats have been funded, while in others, more than 75% of the habitats have been funded. There are also disparities in terms of which habitats are being funded; a quarter of them have never received any funding, while others have been targeted by multiple projects. Transnational cooperation between the states is low, further perpetuating the aforementioned disparities. Projects are implemented almost exclusively within the recipient state, often irrespectively of the conservation status of the targeted habitats in other states. We recommend that the EU addresses these disparities by encouraging projects in underfunded states, especially in habitats with unfavourable conservation statuses. Moreover, the EU should encourage transnational cooperation in order to promote effective conservation across the EU and to help underfunded states build their capacity.