Plant roots and animal guts have developed specialised cells layers to manage mineral nutrient homeostasis that should tolerate the resident microbiota whereas preserving homeostatic integrity. Whether or not and the way the foundation diffusion obstacles within the endodermis, crucial for the mineral nutrient stability of crops, coordinates with the microbiota, is unknown. We reveal that genes controlling endodermal operate within the mannequin plant Arabidopsis thaliana contribute to the plant microbiome meeting. We characterize a regulatory mechanism of endodermal differentiation pushed by the microbiota with profound results on nutrient homeostasis. Moreover, we reveal that this mechanism is linked to the microbiota’s capability to repress responses to the phytohormone abscisic acid within the root. Our findings set up the endodermis as a regulatory hub coordinating microbiota meeting and homeostatic mechanisms.