Background: Roux-en-Y gastric bypass (RYGB) is a highly effective treatment for severe obesity, achieving substantial weight loss and metabolic improvement. Beyond weight, assessing body composition and functional markers is essential. Phase angle (PA), obtained through bioelectrical impedance, is a relevant indicator of cellular integrity and nutritional status. The rise of glucagon-like peptide-1 and glucose-dependent insulinotropic polypeptide (GLP-1 and GLP-1/GIP) agonists makes comparison with surgical outcomes increasingly important. This study aimed to evaluate changes in fat mass, lean mass, hydration, and PA after RYGB and compare these findings with evidence from pharmacological therapies. Methods: A retrospective observational study was conducted in 15 patients (18–50 years, BMI > 35 kg/m²) at Quirón Salud Hospital Torrevieja. Body composition was assessed using multifrequency bioelectrical impedance (TANITA BC-980) before surgery and at 3 and 12 months. All patients received structured nutritional follow-up. Repeated-measures ANOVA and the Friedman test were applied. Results: After 12 months, weight decreased by 40.06 ± 11.86 kg; fat mass by 30.43 ± 10.81 kg; and fat-free mass by 9.64 ± 5.31 kg. PA declined 11% during the first 3 months and then stabilized. Women lost more fat mass; men lost more lean mass. Conclusions: RYGB combined with nutritional support produces high-quality weight loss with relative preservation of lean tissue and stabilization of PA, which proves valuable for postoperative monitoring.