: Pediatric patients with non-IgE-mediated gastrointestinal food allergies (non-IgE-GIFAs) may experience alterations of nutritional status. This non-randomized, prospective intervention study investigated the impact of dietary counseling on nutritional status in pediatric patients with non-IgE-GIFAs. : Patients of both sexes aged 0-14 years newly diagnosed with non-IgE-GIFAs received dietary counseling provided by certified pediatric dietitians immediately after diagnosis. Nutritional status parameters were assessed to identify nutritional status alterations at baseline and after 12 months of intervention (T12). : The study included 100 patients (58% male, mean age 8.5 ± 8.8 months). Non-IgE-GIFAs phenotypes included food protein-induced enteropathy (FPE, 44%), food protein-induced enterocolitis syndrome (FPIES, 11%), food protein-induced allergic proctocolitis (FPIAP, 17%), and food protein-induced motility disorders (FPIMD, 28%). At diagnosis, 1% was affected by obesity (1 FPIAP), 5% were affected by overweight (2 FPE, 1 FPIAP, and 2 FPIMD), 7% were moderately underweight (5 FPE and 2 FPIMD), 1% was severely underweight (1 FPE), 7% were moderately stunted (4 FPE, 1 FPIAP, and 2 FPIMD), 16% were moderately wasted (11 FPE, 1 FPIES, 1 FPIAP, and 3 FPIMD), and 4% were severely wasted (2 FPE and 2 FPIMD). At T12, improvements in anthropometric parameters were observed, along with a reduction in the prevalence of malnutrition by excess (6% at diagnosis vs. 2% at T12) and a reduction in the undernutrition subtypes rate, including underweight, stunting, and wasting (26% at diagnosis vs. 3% at T12, < 0.001). : Non-IgE-GIFAs can negatively impact the nutritional status of pediatric patients. Thus, dietary counseling could be an effective strategy for preventing and managing nutritional alterations in these patients.