Soil microbiota, in particular fungi and bacteria, play a major role in soil quality and functioning, largely determining soil structure, carbon and nutrient cycling, and ultimately impacting plant performance through nutrient mineralization and mobilization, especially for N and P, root growth, plant health, and possibly increasing crop yield under stress conditions, as required to achieve food security in the coming decades. In addition to the rhizosphere microbiome, plants host an endophytic microbiome, and the composition and function of both these microbiomes strongly vary with genotypic differences in plant traits, while different plant genotypes may respond differently to beneficial microorganisms. Focusing on three of the most important European crops (bread wheat, durum wheat and potato), the ground-breaking novelty of the SolACE project was to include such below-ground processes and related traits in the breeding strategies to be implemented throughout the project, on the one hand, and to access the benefit in a range of agroecosystem management innovations and pedo-climatic conditions combining water and N or P deficit on the other hand. This will be important to achieve high crop yields and food quality through more sustainable agricultural practices and increased resource use efficiency via the promotion of plant-microbe interactions and has so far seldom been tackled in breeding programmes.