In the context of highly pressured agricultural production using low levels of inputs, cropping strategies could take advantage of existing plant-microbiome interactions that can improve both plant growth and health. We believe that plant genetics can provide some clues to better understand the mechanisms underlying microbiome recruitment by the plant. The aims of this work were (i) to assess plant genotype effect on the rhizosphere bacterial communities in relation to the plant nutritional strategies for a core collection of 155 genotypes of Medicago truncatula and (ii) to highlight the genetic determinisms potentially associated in these interactions. To achieve these aims, we developed a multidisciplinary approach where the plant growth and nutritional strategies were characterized using an ecophysiological framework, the rhizosphere bacterial communities were described using massive parallel sequencing, and the genetic determinisms were analysed using Genome-Wide-Association Studies. We observed a significant effect of the plant genotype and identified different groups of plant genotypes according to their nutritional strategies and to the structure and composition of their associated rhizosphere bacterial communities. To go further, we also highlighted loci linked to microbiome recruitment by the plant. First, we showed that plant genetics may provide the levers to manipulate soil microflora through plant microbiome recruitment. Then, this work demonstrates the importance of combining approaches from different disciplines to better unravel plant-microbiome interactions.