Abstract Objective The objective of this study was to determine the role of body fat percentage (BFP) changes in diabetes remission (DR) and the association between baseline body composition and its changes after bariatric surgery. Methods We analyzed 203 patients with type 2 diabetes who underwent Roux‐en‐Y gastric bypass. Body composition was measured using a gold‐standard‐derived predictive equation and magnetic resonance imaging. Body composition changes were calculated as 100 × (baseline value – follow‐up value)/baseline value. We verified the results in a laparoscopic sleeve gastrectomy cohort with 311 patients. Results Compared with non‐remission patients in the Roux‐en‐Y gastric bypass cohort, those who achieved DR showed a higher baseline fat‐free mass index (FFMI) and experienced the most significant changes in BFP ( p < 0.001). In comparative analyses, BFP changes were significantly better than BMI changes in identifying short‐ and long‐term DR. Linear regression analysis identified FFMI as the most significant baseline variable correlated with BFP changes ( p < 0.001). Baseline BMI was positively correlated with changes in BFP but negatively correlated with changes in FFMI. These findings were replicated in the laparoscopic sleeve gastrectomy cohort. Conclusions BFP changes determine DR after bariatric surgery, and baseline FFMI is crucial for BFP changes. A low initial BMI is associated with a smaller BFP reduction and greater FFMI loss after bariatric surgery.