Endemic mountain species are highly vulnerable to climate change due to their narrow ecological niches, facing elevated risks of population decline and extinction. Here, we assessed the impacts of climate change on four endemic medicinal and aromatic plant species (Cladanthus scariosus, Globularia nainii, Euphorbia resinifera, and Thymus pallidus) in the Central High Atlas of Morocco. We aimed to (i) model their current distributions, (ii) project future changes under different emission scenarios, and (iii) evaluate climate-driven changes in species richness and interspecific niche relationships. Following a Species Distribution Modelling (SDM) framework, we projected current and future distributions under four Shared Socioeconomic Pathways (SSP1-2.6, SSP2-4.5, SSP3-7.0, SSP5-8.5) across four periods (2021–2040, 2041–2060, 2061–2080, 2081–2100). Our results reveal a general contraction of suitable habitats relative to current ranges, with contrasting patterns among taxa. Under SSP5-8.5, Thymus pallidus and Globularia nainii are the most vulnerable, losing up to 56.2% and 40.9% , while Cladanthus scariosus declines by 39.3%. In contrast, Euphorbia resinifera shows moderate losses (8–20%) under low-emission scenarios but expands under severe conditions. All species exhibit upward elevational shifts, reaching up to 266 m for Cladanthus scariosus, 196 m for Globularia nainii, and 114 m for Euphorbia resinifera. Thymus pallidus showed a more complex response, with moderate upward shifts under low-emission scenarios followed by downward shifts under SSP5-8.5, suggesting a collapse of high-elevation habitats. Climate change is also likely to reshape niche relationships, increasing divergence among most taxa. Additionally, all species exhibit centroid displacements, leading to increased habitats fragmentation and declining endemic richness. Overall, our findings highlight the high vulnerability of these endemic taxa and emphasize the need for conservation strategies focused on enhancing habitat connectivity, assisted migration and domestication of the most vulnerable species, to ensure long-term persistence and sustainable use.