Gastrointestinal infections often induce epithelial damage that must be repaired for optimal gut function. While intestinal stem cells are critical for this regeneration process, how they are impacted by enteric infections remains poorly defined. Here, we investigate infection-mediated damage to the colonic stem cell compartment and how this affects epithelial repair and recovery from infection. Using the pathogen Clostridioides difficile, we show that infection disrupts murine colonic adherens-junctions and crypt polarity, exposing the otherwise protected stem cell compartment, in a TcdB-mediated process. Exposure and susceptibility of colonic stem cells to intoxication compromises their function during infection, which diminishes their ability to repair the injured epithelium, shown by altered stem cell signalling and a reduction in the growth of colonic organoids from stem cells isolated from infected mice. TcdB also targets human colonic organoids, suggesting that gut regeneration during human C. difficile infection may be diminished. We also show that stem cell TcdB intoxication during CDI can occur through different receptors dependent on the TcdB toxin type. Our results uncover a mechanism by which an enteric pathogen subverts repair processes by targeting stem cells during infection and creates an environment in which disease recurrence is likely.