The mucosal immune system regulates the balance of intestinal microflora by innate immunological molecules such as antimicrobial peptides (AMPs). Dectin-1 is the receptor for β-glucans which are a component of fungal cell walls and are contained in various foods, suggesting that Dectin-1 signaling may regulate intestinal mucosal immunity. Here, we found that calprotectin, one of AMPs, was exclusively produced by mouse colonic epithelial cell (cEC), and Dectin-1 deficient mice showed significantly impaired calprotectin expression in cEC. Calprotectin was induced by a special IL-17 family cytokine that was mainly produced by macrophages in colonic lamina propria. Calprotectin specifically suppressed the growth of a species of intestinal commensal bacteria belonging to Firmicutes, and the population of this species was increased in both Dectin-1 and this IL-17 family cytokine deficient mice. Furthermore, the ligand of Dectin-1 in mouse intestine was identified as food-derived β-glucans. These findings suggest that oral administration of β-glucans regulates the balance of commensal bacteria population via the Dectin-1-induced cytokine-dependent AMP secretion to control the homeostasis of intestinal immunity.