Red wolves (Canis rufus) are the most critically endangered wolf globally, with over 95% of individuals living under human care. Gastrointestinal (GI) disease is one of the leading causes of death among adult red wolves under human care, yet links between management practices and this condition remain unclear. By integrating studbook data, survey-based husbandry information, veterinary records, and necropsy reports, our study explored the relationships between management practices and post-mortem diagnoses of GI mucosal disease among 36 adult red wolves between 2004 and 2022. For final diets fed for a minimum of 4 months before death, we report that wolves fed diets limited to only kibble were more likely to exhibit a greater severity of GI mucosal disease than those fed diets that integrated whole prey or other meat items. In addition, while living at their final facilities for a minimum of 9 months before death, wolves treated with a nonsteroidal anti-inflammatory drug exhibited more severe GI issues than those who were not. Conversely, we found no effect of housing and life history traits on GI health. This study highlights the importance of evaluating management and veterinary protocols on red wolf GI health.