A high-fat diet (HFD) induces metabolic disease and low-grade metabolic inflammation in response to changes in the intestinal microbiota through as-yet-unknown mechanisms. Here, we show that a HFD-derived ileum microbiota is responsible for a decrease in Th17 cells of the lamina propria in axenic colonized mice. The HFD also changed the expression profiles of intestinal antigen-presenting cells and their ability to generate Th17 cells in vitro. Consistent with these data, the metabolic phenotype was mimicked in RORγt-deficient mice, which lack IL17 and IL22 function, and in the adoptive transfer experiment of T cells from RORγt-deficient mice into Rag1-deficient mice. We conclude that the microbiota of the ileum regulates Th17 cell homeostasis in the small intestine and determines the outcome of metabolic disease. Display omitted •HFD-induced T2D decreases the number of ileum IL17/RORγt CD4 T cells•IL17/RORγt-deficient CD4 T cells induce T2D and obesity•HFD-induced ileum microbiota dysbiosis lowers intestinal IL17/RORγt-CD4 T cells•HFD reduces antigen presenting cell ability to induce Th17 cell differentiation Obesity and type 2 diabetes have been linked to the gut microbiota. Garidou et al. show that a high-fat diet induces gut microbiota dysbiosis which impairs the intestinal immune defense, including reduced intestinal IL 17 T cells. The intestinal immunity changes precede the onset of diabetes.