This dataset comprises a large array of ecological data for the European Alps: (1) Current soil and climate predictors at various resolutions. (2) GBIF observations of the European Alps Flora (~4,000 species). (3) Species habitat suitability maps (1,109 species; based on species observations filtered at 40x40-km) at various resolutions used in the study to generate (4); except 'expert'... (4) Expert, Taxonomic, phylogenetic and functional diversity of the study region at various resolutions (from 100-m to 40-km --> 100-m aggregated & mean to km + non-aggregated/predicted) for CLIM, SOIL and CLIM-SOIL models. (5) Ecological and altitudinal preferences of the European Alps Flora. (6) Data outputs of the related published article. (7) All scripts used for analyses. (8) Additional files used for analyses. (9) Improved set of species habitat suitability maps (~2,600 species; based on species observations filtered at 1x1-km) and related taxonomic diversity at 100-m resolution (aggregated to km + non-aggregated/predicted) for CLIM, SOIL and CLIM-SOIL models ---> not incorporated in the study.