Purpose The Antarctic Peninsula represents a unique ecosystem characterized by extremely harsh environmental conditions. In this study, we investigated the microbial diversity and functionality of Antarctic soils, focusing on the coexisting rhizosphere microbiomes associated with the only two native vascular plant species, Deschampsia antarctica and Colobanthus quitensis. Methods Soil samples were collected from three sites along an altitudinal transect near Admiralty Bay on King George Island, Antarctic Peninsula. Comprehensive chemical analyses of the soils were performed, followed by DNA extraction and bioinformatic analyses to explore microbial diversity and metabolic functions. Results Our results revealed significant disparities in soil chemical composition across sites, with distinct variations observed in pH, calcium, magnesium, aluminum saturation, cation exchange capacity, and phosphorus concentrations. Despite these differences, taxonomic profiling via metabarcoding indicated relatively homogeneous bacterial communities in terms of alpha diversity but significant differences in beta diversity among the sites. Firmicutes dominated at Site 1, while Proteobacteria predominated at Site 2, and Actinobacteriota at Site 3. Functional prediction analysis revealed diverse metabolic activities within Antarctic soil microbial communities, with heightened fermentation potential in Sites 1 and 2, and notable functions related to aromatic compound degradation and phototrophy in Site 3. Conclusions These findings contribute to our understanding of the intricate dynamics of Antarctic soil microbiomes, highlighting the influence of soil physicochemical properties and plant-microbe interactions on microbial community structures and functions in these extreme environments. Such insights have substantial implications for conservation strategies and the advancement of biotechnological applications in Antarctic ecosystems.