Short bowel syndrome with intestinal failure is a rare disease with a massive impairment in quality of life, requiring a multidisciplinary team approach to medical, surgical, and nutritional therapy. Current pharmacological and surgical therapeutic options are limited; an important cornerstone is enteral and parenteral nutrition. The changed physiology of carbohydrate digestion plays a major role in the adaptation process and can be a target for specific enteral nutrition interventions. An important prognostic factor is the preservation of at least portions of the colon in continuity with small bowel. This strategy has to include an evaluation of the anatomical situation and small bowel absorptive capacity, adaptation processes, and luminal microbiota including its fermentative properties. Starch is probably the most important complex carbohydrate in short bowel syndrome nutrition, because it is absorbed or fermented almost completely. Benefits of supplementation with complex carbohydrates include improved adaptive processes, positive trophic effects on the mucosa and its hormonal response, longer transit time, and possibly a faster time to wean from parenteral nutrition, but supplementation advice needs to weigh carefully the risks and benefits, especially considering bacterial overgrowth, osmotic load, and D-lactate acidosis.