BACKGROUND/OBJECTIVES: Anorexia nervosa (AN) is a severe psychiatric disorder characterized by profound nutritional deficits and significant alterations in body composition, cellular integrity, and hydration. Nutritional rehabilitation is critical not only for weight restoration but also for improving body composition and metabolic functions. However, optimal strategies for integrating caloric and protein intake to achieve balanced recovery remain underexplored. This study aims to evaluate the interactions between caloric/protein intake and time on quantitative (weight and BMI) and qualitative (body composition and cellular health) outcomes, and to identify markers that predict recovery trajectories and guide personalized nutritional interventions. METHODS: This retrospective observational study analyzed 79 patients with AN admitted to Villa Miralago for six months of nutritional rehabilitation. Anthropometric and body composition parameters-including body weight (BW), body mass index (BMI), fat mass (FM), fat-free mass (FFM), body cell mass (BCM), phase angle (PA), and hydration markers (TBW and ECW)-were assessed at baseline (T0), 3 months (T1), and 6 months (T2). Generalized Estimating Equations (GEEs) were used to evaluate the effects of caloric and protein intake over time. RESULTS: Significant increases in BW (+6.54 kg, CONCLUSIONS: This study highlights the importance of a dynamic, marker-based approach to nutritional rehabilitation in AN. Integrating caloric and protein intake with advanced body composition and hydration markers enables personalized interventions and balanced recovery, shifting AN treatment toward a focus on qualitative improvements overweight restoration alone.