Elevational gradients are characterized by major shifts in environmental conditions, reflected through changes in climatic and soil variables. These shifts strongly impact the composition, community structure and specific functional traits of vegetation. Vegetation, in turn, influences soil properties through litter input, root growth and the release of root exudates, thereby influencing soil microbial and faunal communities. Here, we report and briefly describe data of soil and underlying bedrock physical and chemical properties, climatic variables, plant community composition and species abundance, soil microbial diversity and macro and mesofaunal abundance and diversity. Data are provided for 6 elevations (3400–4600 m) ranging from pine forest to alpine prairie. We focused on soil biophysical properties beneath several keystone or community-structuring plant species with different growth forms: (1) tree (Pinus hartwegii Lindl.); shrub (Oxylobus arbutifolius (Kunth) A. Gray and Chionolaena lavandulifolia (Kunth ex Kunth) Benth. & Hook.f. ex B.D.Jacks.); and (3) herb (Lupinus montanus Kunth and Senecio roseus Sch.Bip.). These data are useful for understanding how shifts in abiotic conditions and vegetation communities along an elevational gradient affect soil ecosystem services such as water infiltration, soil aggregation and carbon (C) storage, and modify soil biodiversity. The collected data also provide useful information to understand how alpine vegetation, soil macro- and meso-fauna, and soil bacterial communities may shift under a climate change scenario.