Background: Growth impairment is a major component of pediatric inflammatory bowel disease (IBD), yet the prognostic role of baseline nutritional status remains debated. We assessed the impact of nutritional status at diagnosis on subsequent medical and surgical disease course. Methods: We retrospectively studied 183 children with IBD (84 Crohn’s disease, 99 ulcerative colitis) followed for at least 18 months. Patients were classified at diagnosis using BMI Z-scores as underweight (n = 35), normal weight (n = 123), or overweight/obese (n = 25). Multivariable regression models—adjusted for diagnosis, biological sex, age at diagnosis, and extraintestinal manifestations/comorbidities—evaluated relapse burden, surgical resection, and longitudinal anthropometric recovery at last follow-up. Results: Baseline underweight status was not independently associated with a higher relapse burden or time to first relapse. A sensitivity analysis excluding surgically resected patients showed higher estimated relapse rates for underweight patients, though these did not reach statistical significance. In exploratory analyses, baseline underweight showed a borderline, non-significant association with subsequent surgical resection (adjusted OR 2.68, 95% CI 0.97–7.27; p = 0.056), warranting validation in larger prospective cohorts. Exploratory VEO-IBD analyses were limited by small subgroup size; within UC, a higher crude resection frequency was observed in VEO-UC than in older-onset UC (15.0% vs. 1.3%), but this finding should be interpreted cautiously. At follow-up, 85.7% of initially underweight patients reached normal weight. Higher baseline BMI Z-score was independently associated with higher follow-up BMI Z-score, whereas therapeutic escalation and total relapse burden were not independently associated with follow-up BMI Z-score. Persistent stunting was very rare (1.9%), precluding multivariable analysis. Conclusions: Baseline underweight showed a suggestive but non-significant association with subsequent surgical resection, warranting confirmation in larger prospective cohorts, while it was not independently associated with medical disease instability. Substantial weight recovery occurred during pediatric IBD follow-up. Baseline BMI Z-score was associated with BMI Z-score at follow-up, although substantial between-patient variability remained unexplained.