Bariatric surgery results in rapid weight loss and beneficial metabolic effects, but may have negative effects on the skeleton. The objective of this prospective study was to evaluate changes in bone metabolism in response to bariatric surgery with two surgical techniques. 46 morbidly obese subjects (mean 44.9 years, BMI 42.1) with (n = 19) or without (n = 27) type 2 diabetes (T2DM) at baseline underwent either Roux-en-Y gastric bypass (RYGB, n = 21) or sleeve gastrectomy (SG, n = 25). Bone turnover markers (CTX, PINP, TRAcP5b, TotalOC and ucOC) were measured before and six months after surgery. Volumetric bone mineral density (vBMD) at lumbar spine and vertebral bone marrow (VBM) fat were measured in 21 subjects (7 RYGB and 14 SG) with three-dimensional quantitative computer tomography and ¹H MR spectroscopy, respectively. 25 non-obese subjects were recruited as controls (mean 45.8 years, BMI 23.0) and assessed at a single cross-sectional visit. Obese subjects had significantly lower bone turnover at baseline when compared to non-obese controls. Bone metabolic markers markedly increased post-operatively (p < 0.0001 for all). The activation of bone remodeling was significantly higher after RYGB than after SG and was particularly observed in patients, whose type 2 diabetes was in remission after weight loss. There was no change in volumetric BMD or marrow fat at lumbar spine six months after surgery in our sample. In conclusion, severe obesity decreases bone remodeling, which is activated after bariatric surgery. The increase in bone turnover after surgery is affected by the choice of surgical technique and by the post-surgery remission of T2DM.