During the anabolic response associated with inflammation, mucin synthesis and colonic protection may be compromised by the limited availability of specific amino acids. We therefore determined the effect of dietary amino acid supplementation on the microbiota, mucin status, and mucosal damage in dextran sulfate sodium (DSS)-treated rats. From 8 d before to 28 d after colitis induction, male Sprague-Dawley rats (10 mo old, n = 8/group) were fed a control diet supplemented or not with 2 different doses of an amino acid cocktail containing L-threonine, L-serine, L-proline, and L-cysteine. All diets were isonitrogenous (adjusted with L-alanine). The higher dose of amino acids increased the number of Muc2-containing goblet cells in the surface epithelium of the ulcerated area, stimulated mucin production in the colon, and restored the mucin amino acid composition and mucosal content to healthy, control values. The colonic mucin synthesis rate was specifically stimulated by 95%, whereas the protein turnover was unchanged. All bacterial populations, markedly altered by the DSS treatment, were promoted. In conclusion, in inflammatory situations, an increase in threonine, serine, proline, and cysteine dietary supply can promote mucin synthesis, reequilibrate the gut microbiota, and thus favor colonic protection and mucosal healing.