Abstract In the intestinal immune system, anatomical and physiological distinctions in the gut contribute to its regional specialization by microbiota and immunomodulatory agents from the diet. Given that the ileal Peyer’s patch (PP) belongs anatomically to the small intestine, while it is physiologically exposed to an environment similar to the large intestine with respect to microbes and microbial metabolites, its characteristics may differ from those in PPs in the jejunum. As the terminal ileal PP is a key mucosal organ where host defense and oral immune tolerance in the gut develop, identification of the specific factors regionally specialized in the tissue is essential to understand mucosal homeostasis. Among the various cell types present in PPs, group 3 innate lymphoid cells (ILC3s) are closely associated with the regulation of commensal bacteria through the suppression of commensal bacteria-specific CD4+ T cells, although the regulation of ILCs in ileal PPs is poorly defined. In this study, we found that butyrate plays a role as a regional specific factor involved in the repression of ILC3s in PPs of the terminal ileum. This butyrate-mediated negative regulation of ILC3s alleviates the tolerogenic mucosal microenvironment by suppressing regulatory T cells in PPs. Collectively, we conclude that the inhibition of ILC3s by microbiota-derived butyrate can confer the functional ability to induce antigen-specific immunity, and that this network contributes to homeostatic regulation of the mucosal immune inductive site.