Background: Obesity is a significant public health issue with increasing global prevalence. Bariatric surgery is currently the most effective intervention for sustained weight loss and improvement in obesity-related comorbidities. This study aimed to compare anthropometric and body composition changes over 24 months following three bariatric procedures, mini-gastric bypass (MGB), sleeve gastrectomy (SG), and Roux-en-Y gastric bypass (RYGB), in an Iranian population. Methods: This study was performed on 6,390 patients who underwent MGB, SG, or RYGB between 2020 and 2022 in Tehran. Anthropometric indices and body composition variables [body mass index (BMI), excess weight loss percentage (EWL%), fat mass, visceral fat, and muscle mass] were measured before surgery and at 3, 6, 12, and 24 months after surgery. Generalized estimating equations (GEEs) were used to assess longitudinal changes and associated factors. Results: All procedures led to significant BMI and EWL% reductions over time (P<0.001). Compared with SG, MGB was associated with a greater BMI reduction and EWL% increase. No significant differences were found in fat mass or visceral fat between the groups, but males showed greater reductions over time. Muscle mass was better preserved in RYGB patients, especially among males. Age and sex were also significant predictors of postsurgical outcomes. Conclusion: Compared with SG, MGB resulted in superior weight loss. RYGB was more effective in preserving muscle mass. Patient characteristics such as age and sex influence surgical outcomes and should be considered in personalized postoperative care.