Mice lacking telomerase (e.g. mTR-/-) for several generations develop dysfunctional telomeres and severe gastrointestinal pathology. Intestinal stem cell (ISC) abnormalities in late-generation mTR mice have been described, and we set out to characterize it in more detail. Expression profiling of mTR-/- crypts and an unbiased gene set enrichment analysis revealed broadly decreased expression of Wnt pathway genes in crypt epithelia and underlying stroma. We describe abnormalities in the Wnt-dependent intestinal stem cell (ISC) niche in these mice, including decreased expression of ISC marker genes Ascl2, Lgr5, and Sox9. The importance of these changes was revealed by rescue of crypt apoptosis along with Ascl2 and Sox9 expression upon treatment of mice with Wnt pathway agonists, as well as enhanced survival and Lgr5 expression in cultured mTR-/- intestinal crypts. Rescue was associated with reduced telomere-dysfunction induced foci (TIFs) and anaphase bridges, indicating improved telomere capping, which correlates with upregulation of Trf2 and Pot1a, encoding capping proteins in the shelterin complex. Similar gene expression changes, and rescue by Wnt pathway activation, were observed in human cells suffering from telomere dysfunction, including those derived from dyskeratosis congenita and Werner syndrome patients. These findings are independent of previously suggested connections between Wnt and the catalytic component of telomerase, TERT, and demonstrate a mutually reinforcing relationship between telomere capping and Wnt signaling, which may provide new approaches to diseases characterized by telomere dysfunction.