Selenium-enriched proteins are the primary form of selenium in plants and animals. Selenium-containing proteins contain various selenoamino acids, including selenocysteine, selenocystine, methyl selenocysteine and selenomethionine, which exert antioxidant, cognitive-enhancing, blood glucose regulating, and immunomodulatory effects. In addition, selenium-enriched proteins play a significant role in the treatment of inflammatory bowel disease by modulating immune activity, repairing the intestinal barrier and maintaining intestinal flora balance. This article reviews the functional properties and species of food-borne selenium-enriched proteins and the methods for their quantitation, focusing on their bioactive mechanisms and synergistic effects with other nutrients. Meanwhile, this review presents an outlook on their potential for application in the treatment and alleviation of inflammatory bowel disease, with a view to providing precise theoretical support for the functional development of selenium-enriched proteins.