Background: Nut allergies are among the most common pediatric food allergies, often persisting into later life and posing significant clinical risks. The likelihood of developing tolerance varies, and identifying predictors of persistence or resolution is essential. This study evaluates clinical and laboratory features of children with nut allergy, comparing data at diagnosis and follow-up to identify factors influencing tolerance, anaphylaxis, and cross-reactivity. Methods: In this retrospective, cross-sectional study, 121 children (0–18 years) diagnosed with nut allergy at a tertiary allergy center between 2016 and 2024 were analyzed. Data included allergic reaction history, comorbidities, total IgE, eosinophil counts, and prick-to-prick test (PTP) wheal sizes. Tolerance was defined based on oral food challenge, absence of reactions upon re-exposure, and clinical follow-up. Results: Multiple nut allergy was present in 81% of patients, with hazelnut (67%) and pistachio (62%) being most common. IgE-mediated reactions were predominant (91%), including urticaria (79%) and anaphylaxis (36%). During follow-up, 25% of patients developed tolerance, while 13% continued to experience anaphylaxis. Aeroallergen sensitisation, particularly to pollens, was significantly associated with reduced tolerance in almond and walnut allergy (p < 0.05). Persistent multi-nut allergy correlated with higher anaphylaxis risk (p < 0.01). Strong cross-reactivity was observed between pistachio–cashew (r = 0.686) and peanut–legumes (r = 0.787). Importantly, smaller PTP wheal sizes at diagnosis were predictive of tolerance (p < 0.05). Conclusion: Tolerance in pediatric nut allergy remains limited, especially in children with multi-nut and aeroallergen sensitisation. Baseline PTP wheal size and aero-sensitisation status emerged as significant and practical predictors of long-term allergy outcomes. These findings emphasize the clinical value of early immunological profiling in risk stratification and support routine re-evaluation in sensitised children to prevent overt dietary restrictions.