Mice lacking the flagellin receptor toll-like receptor 5 (TLR5) exhibit altered gut microbiota composition, low-grade inflammation, metabolic syndrome, and proneness to colitis. However, relative roles of epithelial versus dendritic cell TLR5 in mediating these phenotypes have not been well defined. Further, a recent study suggests this reflects animal husbandry practices rather than loss of TLR5. Therefore, we generated mice lacking TLR5 specifically in intestinal epithelial cells (IEC) or dendritic cells (DC) using a breeding scheme that allowed comparison with sibling controls. Mice with LoxP sites flanking the TLR5 gene were generated on a pure C57BL/6 background and crossed to mice expressing Villin- or CD11c-CRE to generate mice lacking TLR5 in, respectively, IEC (TLR5DIEC) or DC (TLR5DDC). Upon weaning, mice were housed by sex and genotype or sex only (i.e., genotypes cohoused). Responses to purified flagellin, basal phenotype, microbiota composition, and several challenge phenotypes were examined. Loss of IEC TLR5 largely recapitulated basal phenotypes of complete TLR5 deficiency, in both housing conditions. Relative to their sibling controls, TLR5DIEC exhibited low-grade inflammation, metabolic syndrome, inability to efficiently clear pathobionts, and predisposition to colitis. Development of such pro-inflammatory phenotypes associated with alterations in microbiota localization, composition, and inherent pro-inflammatory potential. Basal phenotypic differences between TLR5DIEC and sibling controls were eliminated by antibiotic treatment. In contrast, loss of DC-TLR5 eliminated flagellin-induced IL-22 production but did not result in observable basal phenotypes. DC TLR5 exclusively mediates flagellin-induced IL-22 production. IEC TLR5 is critical for keeping the microbiota in-check to minimize risk for developing diseases associated with intestinal inflammation.