<jats:title>Abstract</jats:title><jats:p>The physiological stresses that diminish tissue stem-cell characteristics remain largely unknown. We previously reported that type I interferon (IFN), which is essential for host antiviral responses, is a physiological stressor for hematopoietic stem cells (HSCs) and small intestinal stem cells (ISCs) and that interferon regulatory factor-2 (IRF2), which attenuates IFN signaling, maintains their stemness. Here, using a dextran sodium sulfate (DSS)-induced colitis model, we explore the role of IRF2 in maintaining colonic epithelial stem cells (CoSCs). In mice with a conditional <jats:italic>Irf2</jats:italic> deletion in the intestinal epithelium (hereafter <jats:italic>Irf2</jats:italic><jats:sup><jats:italic>ΔIEC</jats:italic></jats:sup> mice)<jats:sub>,</jats:sub> both the number and the organoid-forming potential of CoSCs were markedly reduced. Consistent with this finding, the ability of <jats:italic>Irf2</jats:italic><jats:sup><jats:italic>ΔIEC</jats:italic></jats:sup> mice to regenerate colon epithelium after inducing colitis was severely impaired, independently of microbial dysbiosis. Mechanistically, CoSCs differentiated prematurely into transit-amplifying (TA) cells in <jats:italic>Irf2</jats:italic><jats:sup><jats:italic>ΔIEC</jats:italic></jats:sup> mice, which might explain their low CoSC counts. A similar phenotype was induced in wild-type mice by repeated injections of low doses of poly(I:C), which induces type I IFN. Collectively, we demonstrated that chronic IFN signaling physiologically stresses CoSCs. This study provides new insight into the development of colitis and molecular mechanisms that maintain functional CoSCs throughout life.</jats:p>