Endobarrier® is a minimally invasive, reversible endoscopic treatment for obesity. It provokes malabsorption along 60 cm of the small intestine, which can contribute to the development of vitamin deficiencies and to changes in bone mineral density (BMD). To determine the prevalence of nutrient deficiencies, changes in body composition and BMD during the first year after Endobarrier® placement. Twenty-one patients with type 2 diabetes met inclusion criteria. Levels of vitamins, micro and macronutrients were assessed prior and at 1, 3 and 12 months post-operatively. DEXA was performed before and 12 months after implant. Nineteen patients completed the 12 months follow-up. Vitamin D deficiency was the most prevalent finding before Endobarrier® implant. The percentage of patients with severe deficiency decreased from 19 to 5% at 12 months after supplementation. Microcytic anaemia was initially present in 9.5% of patients and increased to 26.3% at 12 months. Low ferritin and vitamin B12 levels were observed in 14.2 and 4.8% of patients before the implant and worsened to 42 and 10.5%. Low concentrations of magnesium and phosphorus were also common but improved along the study. A significant but not clinically relevant decrease in BMD of 4.14 ± 4.0% at the femoral neck was observed at 12 months without changes in osteocalcin levels. Vitamin deficiencies are common after Endobarrier® implant. It is therefore important to screen patients prior to and at regular intervals after the implant, and to encourage adherence to diet counselling and supplementation.