Mountain ecosystems were early identified as potentially sensitive to global change. In particular, mountain regions may experience unprecedented rates of warming during the next century, two or three times higher than records of the 20th century. Mountain regions are also experiencing changes in land use practice. Species distribution models (SDM) have become essential tools to predict potential effects of climate and landuse changes on species distribution. Yet, despite great progress since its origin, the SDM approach still required further improvement in mountain areas. Here, using the Western Swiss Alps as model region, we assessed several new avenues, including the development of new predictors, effect of scale, model transferability, and species dispersal. Ultimately, we show that, based on the most severe A1FI climate change scenario for 2100 and most realistic simulations in the Western Swiss Alps, one third (28.5%) of the 287 plant species could be at risk of extinction. Results from our dynamic simulations in time also show that first extinctions should not be expected before 2040. By comparing our local predictions to those from coarse continental models, we also highlight the importance of running fine scale and regional assessments, using as proximal as possible predictor variables, in the case of mountain landscapes. Next steps include understanding processes and rules of species assembly in mountain landscapes, as a way to predict the future diversity and composition of communities and how changes in these may affect the functioning of mountain ecosystems. In particular, biotic and abiotic soil characteristics, and their evolution, may play a crucial role in shaping current and future communities, but require a deeper assessment.