<b><i>Background:</i></b> Currently, the two most common bariatric procedures are laparoscopic sleeve gastrectomy (LSG) and laparoscopic Roux-en-Y gastric bypass (LRYGB). Long-term data comparing the two interventions in terms of their effect on body composition and bone mass density (BMD) are scarce. <b><i>Objective:</i></b> The aim of this study was to assess body composition and BMD at least 5 years after LSG and LRYGB. <b><i>Setting:</i></b> Department of Endocrinology and Nutrition, St. Claraspital Basel and St. Clara Research Ltd., Basel, Switzerland. <b><i>Methods:</i></b>Bariatric patients at least 5 years after surgery (LSG or LRYGB) were recruited, and body composition and BMD were measured by means of dual-energy X-ray absorptiometry. Data from body composition before surgery were included in the analysis. Blood samples were taken for determination of plasma calcium, parathyroid hormone, vitamin D<sub>3</sub>, alkaline phosphatase, and C-terminal telopeptide, and the individual risk for osteoporotic fracture assessed by the Fracture Risk Assessment Tool score was calculated. After surgery, all patients received multivitamins, vitamin D<sub>3</sub>, and zinc. In addition, LRYGB patients were prescribed calcium. <b><i>Results:</i></b> A total of 142 patients were included, 72 LSG and 70 LRYGB, before surgery: median body mass index 43.1, median age 45.5 years, 62.7% females. Follow-up after a median of 6.7 years. For LRYGB, the percentage total weight loss at follow-up was 26.3% and for LSG 24.1% (<i>p</i> = 0.243). LRYGB led to a slightly lower fat percentage in body composition. At follow-up, 45% of both groups had a T score at the femoral neck below –1, indicating osteopenia. No clinically relevant difference in BMD was found between the groups. <b><i>Conclusions:</i></b>At 6.7 years after surgery, no difference in body composition and BMD between LRYGB and LSG was found. Deficiencies and bone loss remain an issue after both interventions and should be monitored.