Alpha-ketoglutarate (AKG) is one of the key metabolites that play a crucial role in cellular energy metabolism. Bariatric surgery is a life-saving procedure, but it carries many gastrointestinal side effects. The present study investigated the beneficial effects of dietary AKG on the structure, integrity, and absorption surface of the small intestine after bariatric surgery. Male 7-week-old Sprague Dowley rats underwent gastric bypass surgery, after which they received AKG, 0.2 g/kg body weight/day, administered in drinking water for 6 weeks. Changes in small intestinal morphology, including histomorphometric parameters of enteric plexuses, immunolocalization of claudin 3, MarvelD3, occludin and zonula ocludens 1 in the intestinal mucosa, and selected hormones, were evaluated. Proliferation, mucosal and submucosal thickness, number of intestinal villi and Paneth cells, and depth of crypts were increased; however, crypt activity, the absorption surface, the expression of claudin 3, MarvelD3, occludin and zonula ocludens 1 in the intestinal epithelium were decreased after gastric bypass surgery. Alpha-ketoglutarate supplementation partially improved intestinal structural parameters and epithelial integrity in rats undergoing this surgical procedure. Dietary AKG can abolish adverse functional changes in the intestinal mucosa, enteric nervous system, hormonal response, and maintenance of the intestinal barrier that occurred after gastric bypass surgery.