Patients with inflammatory bowel disease (IBD) suffer of body weight loss, malnutrition, and several other metabolic alterations affecting their quality of life. The aim of this study was to investigate metabolic changes that may occur during acute and chronic colonic inflammation induced by dextran sulphate sodium (DSS) in mice. Clinical symptoms and inflammatory markers revealed the presence of an ongoing inflammatory response in the DSS-treated mice. Mice with acute inflammation had decreased body weight, respiratory exchange ratio (RER), food intake and body fat content. Mice with chronic inflammation had decreased nutrient uptake, body fat content, locomotor activity, metabolic rate and bone mineral density. Despite this, the body weight, food and water intake, lean mass and RER of these mice returned to values similar to those in healthy controls. Thus, murine experimental colitis is associated with significant metabolic alterations similar to IBD patients. Our data show that the metabolic responses during acute and chronic inflammation are different, although the metabolic rate is reduced in both phases. These observations suggest compensatory metabolic alterations in chronic colitis resulting in healthy appearance despite gross colon pathology.