Background It is still debated whether differences in bone turnover markers (BTMs) exist between the 2 most popular bariatric surgery procedures (Roux-en-Y gastric bypass [RYGB] and sleeve gastrectomy [SG]). Objectives To compare changes in BTMs after RYGB and SG, and to investigate their association with predefined markers of interest. Setting University hospital, Lille, France. Methods An ancillary investigation of a prospective cohort was conducted. SG patients with severe obesity ≥40 years were matched one-to-one to RYGB patients for age, sex, body mass index (BMI), and menopausal status. BTMs, as well as predefined markers of interest, were measured at baseline, 12, and 24 months after bariatric surgery. Results Sixty-four patients (66% women) had a mean (standard deviation [SD]) age of 49.6 years (5.1) and a mean (SD) BMI of 45.0 kg/m2 (6.0). From baseline to 12 months, a significant increase in BTMs was observed in both groups (P < .001). Moreover, RYGB was associated with a greater increase in C-terminal telopeptide (β-CTX) and procollagen type 1 N-terminal propeptide (PINP) compared with SG (P < .0001). From 12 to 24 months, a significant decrease in BTMs was observed in both groups, but no significant differences were found between RYGB and SG. However, BTMs did not return to baseline levels. The changes in PINP and β-CTX at 12 months were independently associated with the type of surgical procedure, after adjusting for weight or each predefined marker of interest (all P < .0001). Conclusion RYGB was associated with a greater increase in BTMs than SG at 12 and 24 months.