Disorders of the hepatobiliary system are commonly associated with gastrointestinal (GI) diseases. The GI and hepatobiliary systems interact through the portal vein system and enterohepatic circulation, creating a gut-liver axis that allows for a complex multidirectional interplay between immune, hormonal, dietary and environmental luminal factors that include the gut microbiota. This interaction may underlie the liver affection in autoimmune and immune-mediated small bowel diseases through a variety of pathways that include autoimmune, metabolic, immune-mediated, and/or iatrogenic mechanisms. Despite evidence of a gut-liver axis and co-morbid liver associations with small bowel diseases, the clinical implications and how these conditions should be clinically managed remain unclear. In this narrative review, we describe the hepato-biliary manifestations associated with chronic immune-mediated enteropathies of the small bowel in adults, with particular focus on CeD and Crohn's disease.