Mountain areas are highly structured habitats where elevation, parent material and slope as well as several climatic parameters like temperature, exposure towards solar radiation, wind, and precipitation, change even on a short spatial scale. The great variety makes mountain areas to hotspots for biodiversity. Soil microorganisms of the alpine ecosystems are adapted to prevailing harsh and oligotrophic conditions and their diversity and community composition is impacted by many, site-specific abiotic (as mentioned above) and biotic properties (e.g., vegetation, soil fauna). However, the key drivers for microbial diversity in alpine soils are still under debate. Here, we aim to i) examine the prokaryote and fungal diversity of soils across the Eastern Alps, ii) link the microbial diversity and community structure to environmental properties, and iii) identify key environmental drivers of microbial diversity. In this study, 35 soils were sampled across North Tyrol, Austria. The soils comprise different land use types (grassland, forest), parent materials (calcareous, siliceous) and elevational levels (500, 1000, 1500, 2000 m a.s.l.). The sampled sites have been well described within the Tyrolean soil survey network, including biotic (e.g. vegetation cover) and abiotic (geology, soil chemistry) properties. Besides profound chemical soil analysis, prokaryote and fungal community composition was characterized using amplicon sequencing. We found that microbial diversity varied significantly among the sampled soils, depending on land use type, parent material and elevational level. Almost every specific combination of land use, geology, elevation exhibited characteristic prokaryote and fungal key species. Linking the microbial community structures to environmental properties revealed significant impacts of the soil pH and the contents of dissolved organic carbon and water on prokaryotes and fungi.