Methods and compositions are provided that use proline, serine and threonine to promote healing of the intestinal mucosa. A therapeutically effective amount of proline, serine and threonine is administered to an individual in need thereof, for example a human or other mammal, such as an individual that has damaged intestinal mucosa. The methods and compositions can promote mucosal healing, restore gut barrier function, repair intestinal epithelial cells, promote protection of the colonic epithelium, and/or promote the replenishment of goblet cells in the intestinal and colonic mucosa.