Soils in cold and high-elevation environments are complex ecosystems composed of multiple, co-occurring biological entities that each harbor distinct microbial communities. Traditional perspectives often examine soil microbial diversity as separate from the microbial communities of the organisms that inhabit it. Here, we seek to challenge such view and propose an alternative and holistic interpretative framework in which the soil meta-community is the sum of different microbial communities belonging to various organisms found within the soil or interacting with it. Applying this comprehensive view, this study explores soil prokaryote and fungal diversity and the associated microbiota in mammals, invertebrates, and plants in alpine pastures. We sampled soil (Ah horizon), rhizosphere communities (Carex spp., Festuca spp.), soil-dwelling and surface-active invertebrates (nematodes, collembolans, earthworms, beetles), and vertebrates (fecal eDNA of hares, wild ungulates, and livestock) at alpine sites at 2500 m above sea level (a.s.l.). Sampling was conducted at the Long-Term Socio-Ecological Research (LTSER) site Matsch/Mazia (Italy), a model site for studying climate- and land-use-driven change in the European Alps. We compared these high-elevation microbial communities with those from lower alpine pastures to evaluate how climate-related environmental conditions shape microbial interconnectedness.Our results show that, beyond climatic and edaphic factors, biotic factors, especially the presence of living organisms like animals and plants, significantly shape microbial diversity in alpine soils. Analyses of fungal and bacterial taxa shared among sample types established greater overlaps between microbiota of soil, rhizosphere, and soil-dwelling invertebrates, compared to that of other invertebrates and vertebrates. This finding highlights the central role of soil microbiota and the above- and belowground as well as host- and habitat-specific associations in the alpine meta-community. Importantly, microbial interconnectedness was lower at 2500 m a.s.l. compared to lower elevations, reflecting reduced microbial exchange among soil and animal-associated communities.Overall, our findings highlight that cold ecosystems host tightly interlinked, but increasingly fragmented, microbiota. Recognizing soils as meta-communities provides new insights into how climate-driven changes in alpine environments may restructure biodiversity and ecosystem functioning.