Exercise has been suggested as a therapeutic approach to attenuate bone loss induced by bariatric surgery (BS), but its effectiveness remains unclear. Our aim was to determine if an exercise‐training program could induce benefits on bone mass after BS. Eighty‐four patients, submitted to gastric bypass or sleeve gastrectomy, were randomized to either exercise (EG) or control group (CG). One month post‐BS, EG underwent a 11‐month supervised multicomponent exercise program, while CG received only standard medical care. Patients were assessed before BS and at 1, 6, and 12 months post‐BS for body composition, areal bone mineral density (BMD), bone turnover markers, calciotropic hormones, sclerostin, bone material strength index, muscle strength, and daily physical activity. A primary analysis was conducted according to intention‐to‐treat principles and the primary outcome was the between‐group difference on lumbar spine BMD at 12 months post‐BS. A secondary analysis was also performed to analyze if the exercise effect depended on training attendance. Twelve months post‐BS, primary analysis results revealed that EG had a higher BMD at lumbar spine (+0.024 g∙cm⁻² [95% confidence interval (CI) 0.004, 0.044];​ p = .015) compared with CG. Among total hip, femoral neck, and 1/3 radius secondary outcomes, only 1/3 radius BMD improved in EG compared with CG (+0.013 g∙cm⁻² [95% CI 0.003, 0.023];​ p = .020). No significant exercise effects were observed on bone biochemical markers or bone material strength index. EG also had a higher lean mass (+1.5 kg [95% CI 0.1, 2.9];​ p = .037) and higher number of high impacts (+51.4 [95% CI 6.6, 96.1];​ p = .026) compared with CG. In addition, secondary analysis results suggest that exercise‐induced benefits may be obtained on femoral neck BMD but only on those participants with ≥50% exercise attendance compared with CG (+5.3% [95% CI 2.0, 8.6];​ p = .006). Our findings suggest that an exercise program is an effective strategy to ameliorate bone health in post‐BS patients.