Root exudates play an essential role in helping plants to cope with abiotic stress. However, the modulation of root exudation profiles under multiple stress conditions is still poorly understood. Using targeted and untargeted metabolomics, here we tested the effect of drought, heat stress, and their combination on 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 relates the root exudation profile with the rhizosphere bacterial community, enabling us to dissect the interactions between specific root exudates and bacterial taxa. The composition of root exudates undergoes distinct modulation according to the single or combined stress and to the root zone, but not according to the root type. In addition, we found that stress-specific exudates can influence the relative abundance of specific bacterial taxa, some of which are known to be beneficial microorganisms. Our results contribute to the understanding of plant-soil interactions under the influence of abiotic stressors, which is key in paving the way towards an increased resilience to abiotic stresses, representing a powerful tool to craft the next generation of agricultural practices. Display omitted •Drought, heat, and their combination have a specific influence on root exudation.•The combination of stresses influences exudates differently from the single stresses.•Changes in root exudation are associated with changes of specific microbial taxa.