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Berberine, an isoquinoline quaternary alkaloid, is a molecule with significant therapeutic adaptability. It has been identified, isolated, and measured in a wide range of plant families and species. Of these, Berberis stands out as a significant natural source of berberine, with Berberis vulgaris (B. vulgaris) bark being one of the most notable. The numerous health benefits associated with berberine include its potential use in the treatment of diseases, such as cancer, cardiovascular diseases, diabetes, and neurological disorders. The principal use of berberine has been for its antidiarrheal properties, which may have several modes of action. Its potent antioxidant and anti-inflammatory effects are responsible for its preventive action against stomach ulcers, and it has been found to kill dangerous gut bacteria while boosting the species and numbers of health-promoting bacteria. It protects the colon by influencing the production of several immune factors in addition to upregulating the Wnt-β creatinine signaling cascade. Berberine has shown its potential in regulating cholesterol metabolism by elevating the levels of low-density lipoprotein receptor in the liver. This review comprehensively examines the pharmacokinetics, multifaceted bioactivities, and gut-protective roles of berberine, providing a detailed analysis of its diverse physiological functions and potential clinical applications to advance the understanding and management of gastrointestinal diseases.