Background/Objectives: Celiac disease (CD) alters nutrient absorption and body composition, especially during childhood. Although adherence to a gluten-free diet (GFD) promotes mucosal recovery, its impact on cellular functionality and metabolic balance remains underexplored. This study aims to evaluate the utility of bioelectrical impedance vector analysis (BIVA) in assessing nutritional status, inflammatory improvement, and body composition changes in pediatric patients with CD following a GFD. Methods: Seventy-nine children aged 5–14 years were studied. Three groups were analyzed: (1) 25 children with newly diagnosed CD, evaluated at diagnosis and after 12 months of GFD (prospective cohort); (2) 25 CD patients on a GFD for over 24 months (cross-sectional); and (3) 29 healthy controls. Body composition (fat mass (FM), fat-free mass (FFM), body cell mass (BCM), phase angle (PhA), and Na⁺/K⁺ ratio) was measured. GFD adherence was assessed and a dietary assessment was also performed. Results: After 12 months on a GFD, newly diagnosed CD patients showed significant increases in FM (from 8.2 to 10.1 kg, p = 0.001), FFM (p = 0.001), and BCM (p = 0.0001), along with a significant decrease in the Na⁺/K⁺ ratio (p = 0.015). Compared to healthy controls, CD children on GFD for more than 24 months had higher FM (12.2 vs. 8.8 kg, p = 0.013) and lower Na⁺/K⁺ ratios (p = 0.006). PhA increased slightly over time but did not reach statistical significance. Conclusions: Our study suggests that the adherence to a GFD leads to improved body composition and cellular homeostasis in children with CD, as reflected by increases in BCM and reductions in Na⁺/K⁺ ratio, making it a promising biomarker for monitoring inflammation and cellular recovery.