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Summary Background This investigation evaluated the efficacy by which resistance training enhances body composition, metabolic, and functional outcomes for obese patients undergoing a 12-week medically supervised hypocaloric treatment. Methods This was a single-blind, randomized, parallel-group prospective trial. Morbidly obese patients were prescribed a 12-week proprietary very low calorie diet (VLCD) treatment (Optifast®) with supplemental protein (1120 kcals/day) and were placed in one of two groups for 14 weeks: 1) Standard Treatment Control (CON) (n = 5) or 2) Resistance Training (RT) (n = 6). Both groups underwent a pedometer-based walking program; however only RT performed resistance training 3 days/week for 12 weeks. Body composition, resting energy expenditure (REE), neuromuscular function, and serum biomarkers were measured at weeks 0, 6, and 13. Results Both groups exhibited a significant loss of total body mass (TBM) (CON: −19.4 ± 2.3 kg, p = 0.0009 vs. RT: −15.8 ± 1.5 kg, p = 0.0002) and fat mass (FM) (CON: −14.7 ± 1.8 kg, p = 0.0002 vs. RT: −15.1 ± 2.1 kg, p = 0.0002) with no group differences. CON lost 4.6 ± 0.8 kg (p = 0.004) of lean mass (LM) while RT demonstrated no changes. Group differences were found for the relative proportion of total weight-loss due to FM-loss (CON: 75.6 ± 3.4% vs. RT: 96.0 ± 6.0%, p = 0.03) and LM-loss (CON: 24.4 ± 3.2% vs. RT: 4.0 ± 6.5%, p = 0.03). CON demonstrated a 328.6 ± 72.7 kcal/day (−14.3 ± 2.4%) (p = 0.02) decrease in REE while RT exhibited a non-significant decrease of 4.6 ± 1.6% (p = 0.78). RT demonstrated greater improvements in all measures of contractile function and strength when compared to CON (p Conclusion Resistance training was advantageous for weight-loss composition by preservation of LM without compromising overall weight- or fat-loss in morbidly obese men and women undergoing a protein supplemented VLCD. These changes accompanied positive adaptations for resting metabolism and muscular function.