A major challenge facing agriculture in the 21st century is the need to increase the productivity of cultivated land while reducing the environmentally harmful consequences of mineral fertilization. The microorganisms thriving in association and interacting with plant roots, the plant microbiota, represent a potential resource of plant probiotic function, capable of conjugating crop productivity with sustainable management in agroecosystems. However, a limited knowledge of the organismal interactions occurring at the root–soil interface is currently hampering the development and use of beneficial plant–microbiota interactions in agriculture. Therefore, a comprehensive understanding of the recruitment cues of the plant microbiota and the molecular basis of nutrient turnover in the rhizosphere will be required to move toward efficient and sustainable crop nutrition. In this chapter, we will discuss recent insights into plant–microbiota interactions at the root–soil interface, illustrate the processes driving mineral dynamics in soil, and propose experimental avenues to further integrate the metabolic potential of the plant microbiota into crop management and breeding strategies for sustainable agricultural production.