Synthetic phosphate fertilizers are frequently used in agriculture and their overuse can significantly increase production costs and cause negative environmental impacts. Soil phosphorus (P) availability can be increased by the contribution of the rhizosphere microbiota associated with the plant root system. This work aimed to evaluate the effect of different phosphate fertilization conditions on maize and sorghum genotypes. Four commercial genotypes of maize and four of sorghum were cultivated for two seasons under seven treatments, no addition of P fertilizer, and 50 and 100 kg P2O5 ha−1 of two rock phosphate (Itafós and OCP) and triple superphosphate. During flowering time, the root system was collected according to the Shovelomics’ method and analyzed by a modified version of Digital Imaging of Root Traits (DIRT) system. The modifications made the root system architecture analyses less error-prone and more effective. Moreover, three diversity indices, Shannon-Wiener (H′), Simpson (1-D) and Chao1, were calculated based on the bacteria abundance and richness. The type of crop followed by the genotype and fertilizer were the main factors that affected the root system, grain yield, genetic diversity and abundance of microorganisms. The most productive genotypes had higher root angle and area, increased foraging on the soil surface and P acquisition. Maize presented higher microorganism diversity, root angle and foraging traits while sorghum presented higher abundance of specific taxa, a narrower root angle and smaller foraging. The combined use of less reactive P sources, which could be more soluble over time by the physicochemical processes and soil microbiota activity, together with more efficient genotypes might reduce the amount of soluble phosphate fertilizers applied annually to crops. • The image analysis improvement allowed a better identification of the root system traits. • Crop type, genotype and fertilizer were the main factors that affected root architecture, microorganism diversity and yield. • Maize showed greater rhizosphere bacterial diversity while sorghum presented higher abundance of specific taxa. • Maize presented higher root angle and foraging traits than sorghum. • Best performing genotypes were characterized by a ‘foraging strategy’, i.e., large root area and topsoil foraging.