As diabetes is a major cause of mortality and morbidity in epidemic rates, continuous research is being done on development of foods with anti-diabetic activity. In this study, the influence of gastrointestinal digestion of quinoa protein to release peptides with anti-diabetic potential was investigated. Quinoa protein was subjected to an in vitro simulated gastrointestinal digestion and fractionated by ultrafiltration. Gastric and gastroduodenal digests and peptide fractions were evaluated for dipeptidyl peptidase IV (DPP-IV), α-amylase and α-glucosidase inhibitory activities. Peptides released during the duodenal phase showed the highest inhibitory effects. Three novel peptides derived from 11S seed storage globulin B were identified in the most active fraction by HPLC-MS/MS. These peptides showed ability to inhibit enzymes involved in incretin degradation and digestion of dietary carbohydrates. Therefore, quinoa proteins are promising ingredients of functional foods or nutraceutical applications for the control of diabetes.