AbstractThe intestinal epithelium consists of cells derived from continuously cycling Lgr5hiintestinal stem cells (Lgr5hiISCs) that mature developmentally in an ordered fashion as the cells progress along the crypt‐luminal axis. Perturbed function of Lgr5hiISCs with aging is documented, but the consequent impact on overall mucosal homeostasis has not been defined. Using single‐cell RNA sequencing, the progressive maturation of progeny was dissected in the mouse intestine, which revealed that transcriptional reprogramming with aging in Lgr5hiISCs retarded the maturation of cells in their progression along the crypt‐luminal axis. Importantly, treatment with metformin or rapamycin at a late stage of mouse lifespan reversed the effects of aging on the function of Lgr5hiISCs and subsequent maturation of progenitors. The effects of metformin and rapamycin overlapped in reversing changes of transcriptional profiles but were also complementary, with metformin more efficient than rapamycin in correcting the developmental trajectory. Therefore, our data identify novel effects of aging on stem cells and the maturation of their daughter cells contributing to the decline of epithelial regeneration and the correction by geroprotectors.