Antarctic vascular plants such as Deschampsia antarctica (Da) could generate more suitable micro-environmental conditions for the establishment of other plants like Colobanthus quitensis (Cq). Although positive plant–plant interactions have been shown to contribute to plant performance and establishment, little is known about how microorganisms might modulate those interactions, particularly in stressful environmental conditions. Several reports have focused on the possible ecological roles of microorganisms on vascular plants, but if rhizospheric microorganisms can impact positive interactions among Antarctic plants has been seldom studied. Here, we assessed the physical–chemical characteristics of rhizospheric soils from Cq growing alone or associated with Da (Cq + Da). In addition, we compared the rhizosphere microbiomes associated with Cq, either growing alone or associated with Da (Cq + Da), using a shotgun metagenomic DNA sequencing approach and using eggNOG for comparative and functional metagenomics. Overall, there were no differences among rhizospheric soils in terms of physical–chemical characteristics. On the other hand, our results show significant differences in terms of taxonomic diversity between rhizospheric soils. Functional annotation and pathway analysis showed that microorganisms from rhizospheric soil samples also have significant differences in gene abundance associated with several functional categories related to environmental tolerance and in metabolic pathways linked to osmotic stress, among others. Overall, this study provides foundational information which will allow to explore the biological impact of the rhizobiome and its functional mechanisms and molecular pathways on plant performance and help explain the concerted strategy deployed by Cq to inhabit and cope with the harsh conditions prevailing in Antarctica.