The gastrointestinal tract (GIT) is responsible for essential digestive functions, which rely on tight regulation by a network of neurons and glial cells in the gut wall termed the enteric nervous system (ENS). These cells coordinate numerous gastrointestinal motor, immune and homeostatic functions, which are vital for normal gut activity. Consequently, ENS dysregulation contributes to gastrointestinal disorders and inflammatory bowel disease. In contrast, how ENS dysregulation contributes to infectious gut diseases is less established. Therefore, we aimed to determine if infection with Clostridioides difficile, a pathogen that causes extensive colonic damage, affects the ENS and explore how ENS dysregulation contributes to disease. Using a mouse model of C. difficile infection (CDI), we examined colonic gene expression to assess ENS dysfunction, which showed that colonic genes involved in various ENS processes, neurodegeneration and neurogenesis were differentially expressed during CDI. To link these transcriptional changes to a functional motor alteration, we investigated gastrointestinal transit during disease. Strikingly, CDI slowed intestinal transit, which was further associated with a decrease in the contractive ability of colons. Finally, ENS structure was examined, which showed that CDI greatly disrupted ENS organization thereby linking structural disorder with functional motor alteration. These results demonstrate that CDI considerably perturbs gastrointestinal motility and the ENS, dysregulation of which may then contribute to disease progression. Therefore, this work could aid in the generation of new treatments targeting the ENS to combat disease phenotypes resulting from gastrointestinal infections.