Root exudates play an essential role in plant-soil-abiotic stress interactions. However, we still know little about the influence of stress combinations on the root exudation profile. Using targeted and untargeted metabolomics, here we test the effect of drought, heat stress, and their combination on the maize root exudates, also considering the differences that might exist between root types (seminal and primary) and root zones (apical and sub-apical). In addition, we built an analytical framework that relate the root exudation profile with the characterization of the rhizosphere bacterial community, enabling us to dissect the interactions between specific root exudates and microbial taxa. Our results suggest that the composition of root exudates has a different outcome according to the single or combined stress and to the root zone but not between root types. Further, we found that stress-specific exudates influence the relative abundance of specific microbial taxa, some of which are known to be beneficial microorganisms. Therefore, the stress-specific root exudate composition selecting specific microbial taxa, here observed, represent a contribute on the effects of climate changes on crops increasing thus the potential impact on the current trend of crafting agricultural practices within a wider point of view of plants-microbe-environment interactions.