BACKGROUND Little information exists to guide monitoring and treatment of malnourishment during pregnancy after bariatric surgery. Here we present a case with severe deficiencies and recommendations for testing and treatment. CASE Our patient underwent a duodenal switch procedure resulting in significant weight loss and numerous deficiencies. She then experienced a neonatal demise with multiple congenital abnormalities, including diaphragmatic hernia, possibly related to severe vitamin A deficiency. After high doses of oral and parenteral replacement, pancreatic enzymes, and total parenteral nutrition, she delivered an anatomically normal but growth-restricted neonate in a subsequent pregnancy. CONCLUSION Bariatric procedures may result in nutritional deficiencies that affect pregnancy outcome. Women with severe deficiencies require pre-pregnancy counselling, monitoring, aggressive treatment, and a multidisciplinary approach to care.