The ongoing biodiversity crisis necessitates greater efforts to ensure the adequate conservation of critical habitat types. Even though the identification of protected areas is still required in Europe, conservation efforts are now focusing on management requirements for protected areas and habitat types. Establishing effective management approaches is important for the conservation of the natural and semi-natural habitat types that are identified under the Habitats Directive framework. In this study, we propose a methodology for determining priorities in the conservation management of habitat types based on readily available data. This method relies on four simple criteria to rank habitat types, which includes: conservation condition, biodiversity value, pressure factor, and the cover relevance of habitat types (indicating regional responsibility in terms of area covered). After ranking the habitat types based on the sum of the scores given to all of the criteria, the 25% top-ranking habitat types were prioritized. The pressure factors are analyzed using cluster analysis to better convey information regarding the management needs of groups of habitat types. This prioritization method was tested in habitat types occurring within the Italian Alpine and Continental biogeographical regions. From this analysis, forests, bogs and fens, and dry grasslands were identified as conservation priorities for the Alpine region; meanwhile, a wider variety of habitat types were identified for the Continental region. Important pressure factors were identified (e.g., roads and motorways) for these two biogeographical regions of Italy, which could be used to suggest specific conservation measures. The proposed approach represents a transparent and reliable method for outlining habitat-type priorities based on conservation, biodiversity, pressure, and cover factors, which can be applied to identifying conservation measures that can help achieve biodiversity targets.