Background/Objectives: Long-term comparative data on body composition (BC) trajectories following different bariatric procedures remain limited, particularly regarding potential muscle preservation after malabsorptive techniques. We aimed to compare 5-year changes in adiposity and muscle mass following biliopancreatic diversion (BPD), Roux-en-Y gastric bypass (RYGB), and sleeve gastrectomy (SG), adjusting for baseline heterogeneity. Methods: In this retrospective longitudinal study, 128 patients with severe obesity were followed for 60 months. BC was assessed annually using multi-frequency bioelectrical impedance analysis. Multivariable linear mixed-effects models adjusted for baseline BMI, age, and sex were used to evaluate trajectories of total weight loss (%WL), fat mass loss (%FML), and skeletal muscle mass (SMM). Results: BPD demonstrated a significantly superior longitudinal trajectory for %WL (β = 0.124 [95% CI: 0.013–0.235], p = 0.028) and %FML (β = 0.288 [95% CI: 0.135–0.440], p < 0.001) over 5 years. However, no statistically significant independent differences between techniques were observed at the isolated 60-month endpoint after full adjustment. Although BPD was associated with a higher percentage of muscle mass loss (p = 0.019), absolute skeletal and appendicular muscle mass did not differ significantly across procedures. Age emerged as an independent negative predictor of weight and fat loss (p < 0.001). Conclusions: After rigorous adjustment for baseline characteristics, BPD provides greater long-term adiposity reduction without evidence of disproportionate impairment of absolute muscle mass compared with RYGB or SG. These findings contribute to a more refined understanding of long-term body composition dynamics following bariatric surgery.