Juniperus drupacea is a highly morphologically and genetically differentiated Tertiary relict, displaying a disjunct geographical range in the eastern Mediterranean. Being a thermophilous, light-demanding, and moderately drought-resistant tree, it survived the past climatic oscillations via altitudinal migration. The species has its westernmost range limit, and its only populations in the EU, in Mts Parnon and Taygetos (Greece). These populations are genetically isolated and distinct compared to their Asian counterparts. For Europe, Juniperus drupacea is categorized as an endangered species by the IUCN. Juniperus drupacea forests constitute a priority habitat for conservation in the EU. However, the species’ conservation status has never been assessed in Greece and the same applies to its climate and land-use change assessment. As Greece is already facing the short-term impacts of climate- and human-induced land-use change, studies dealing with the potential long-term climate- and land-use change effects on rare plant species distribution are urgently needed to implement efficient conservation management plans. Our research employs species distribution models, considering multiple climate scenarios and abiotic factors across different timeframes (2020s, 2050s, 2080s), factoring in the potential threat of forest fires. Additionally, we assess the species’ extinction risk at the European level, according to IUCN Criteria A and B. Study findings indicate significant habitat changes and an elevated extinction risk for Juniperus drupacea in Greece. To safeguard this priority habitat, informed conservation strategies, management plans, and policy making are recommended, based on our scientific insights.