Soil microbial communities have an important role in plant establishment and health. Particularly, the role of the soil microbiome in agriculture is of current interest. The study of microbial communities associated with purslane could open questions about the rational exploitation of the microbiota for sustainable agricultural purposes. In this study, the composition of the fungal and bacterial communities and the bacterial metabolic functions, associated with the rhizospheres of two purslane genotypes (one commercially available and one collected from the wild in Spain) were evaluated. The results showed a clear effect of purslane genotype on fungal and bacterial community composition and functional profiles. The bacterial community of the commercial purslane rhizosphere was characterized by more numerous metabolic pathways, mainly pathways related to Terpenoids and Polyketides, Carbohydrate, Lipid, and Amino Acid metabolism. By contrast, the rhizosphere bacterial community of the Spanish (wild) genotype was characterized by the enrichment of functions related to cellular processes such as cell motility and transport. We hypothesize that these differences could be due to differential effects of root exudate composition on the microbial functional community composition. This finding points out the need to consider differences in the functional characteristics of plant genotypes when selecting the beneficial microorganisms to be used as biofertilizers aiming to maximize plant growth and resistance to environmental stressors.