The European Alps are experiencing more than twice the increase in air temperature observed in the rest of the world. Thus, the treeline ecotone, and the unique habitats above it, offer a preview of drastic changes in plant and animal communities. However, our knowledge about climate change impacts on microbial diversity belowground is scarce. Here we investigate how upslope shift of the treeline ecotone, associated with changes in soil nutrient content, temperature and precipitation, will influence alpine ectomycorrhizal (EM) communities of Dryas octopetala, Bistorta vivipara and Salix herbacea across different habitat types in the Alps. We also assessed the degree of EM community taxonomic composition turnover in these habitats across three different climatic projections for 2040 and 2070. Our results indicate that the specialized EM fungal communities from snowbed habitats will be mostly negatively influenced under the current trajectory of environmental shifting predicted for the region. In contrast, fungi from the treeline ecotone, having wider niches, will be positively influenced by future climate and extend upwards. In addition, our predictions of EM community turnover for putative future climatic scenarios revealed high rates of turnover across the entire alpine region. This, together with glacier retreats, will aid colonization of alpine snowbed habitats by new EM plants and associated fungi, bringing additional pressures on local mycorrhizas and likely leading to fungal species extinctions.