Abstract Background Food protein‐induced enterocolitis syndrome (FPIES) is a non‐IgE‐mediated food allergy with predominant gastrointestinal symptoms. The aim of this study was to analyze the various clinical phenotypes and outcomes of FPIES among children in Switzerland. Methods A prospective observational study was conducted across four pediatric clinics in Switzerland from 2019 to 2024. Results Ninety‐eight children were enrolled in this study, with a total of 121 FPIES diagnoses. Common trigger foods in acute FPIES included cow's milk ( n = 26), hen's egg ( n = 22), fish ( n = 20), meat ( n = 17), and vegetables ( n = 12). Acute FPIES to a single food was the most frequent phenotype ( n = 86, 71%). Chronic FPIES occurred in 17 cases (14%). Among acute FPIES cases ( n = 104, 86%), 18 exhibited multiple triggers, and 17 were classified as atypical FPIES. In a small subgroup, FPIES with phenotype switch to an IgE‐mediated food allergy was observed. These cases were associated with cow's milk as trigger and markedly elevated specific IgE levels. Survival analysis revealed a median age of resolution of 11 months in children with chronic FPIES, and 4.8 years in children with acute FPIES with great variety across different foods (1.6 years for cow's milk, 4 years for hen's egg, 4.8 years for meat, and 10 years for fish). Conclusion In this Swiss cohort of children with FPIES, we identified the predominant trigger foods and characterized distinct phenotypic presentations, the most common being acute FPIES to a single food. Tolerance development was dependent on trigger foods and specific clinical phenotypes.