In Europe, the world's largest network of protected areas - Natura 2000 (N2000) - has been implemented to protect Europe's biodiversity. N2000 is built upon two cornerstones, the Birds Directive and the Habitats Directive (HD), which lists 230 bird species and 230 habitat types, respectively, to be protected. Despite the N2000 sites designated to date are reported to represent the target species and habitats quite well, especially in the terrestrial realm, European biodiversity is still on a steady decline. This leaves us wondering how effective current N2000 sites are; a question that has led to ambigious results for the species part of the directive, while the habitats' representativeness has received very little attention in the scientific literature altogether. Here we developed a generic workflow, which we exemplified for Germany, to assess the status of habitat coverage within the N2000 network, combining information from publicly available data sources. Applying the workflow allows identifying gaps in habitat protection, followed by the prioritization of potential areas of high protection value, using the conservation planning software Marxan. We found that, in Germany, N2000 covers all target habitats. However common habitats were proportionally underrepresented relative to rare ones, contrasting comparable studies for species. Moreover, the German case study suggests that especially highly protected planning units (i.e. areas covered by more than 90% with N2000 sites) build an excellent basis towards a cost-effective and efficient conservation network. Our workflow provides a generic approach to deal with the popular problem of missing habitat data outside of N2000 sites, information which is however crucial for managers to plan conservation action appropriately across Europe. To avoid a biased representation of habitat types within N2000, our results underpin the importance of defining more tangible targets which will allow assessing the trajectory of habitat protection in Europe as well as adjusting the network accordingly - a future necessity in the light of climate change.