To meet the COP15 biodiversity framework in Europe, one target is to protect 30% of land by 2030 through a resilient transnational conservation network 1,2. The European Alps are a key hub of this network hosting one of the most extensive natural areas and hotspots of plant biodiversity in Europe 3,4. Here, we assess the robustness of the conservation network to safeguard the European Alps’ flora by 2080 using semi-mechanistic simulations. Overall, we predict a shift in conservation need from lower to higher elevations through time as plants migrate upslope and shrink their distribution. While increasing species, trait, and evolutionary diversity, migration could also threaten 70% of the resident flora. Future expansions of the protected area network should ensure strong elevational connections, even those that span borders.