Cow's milk allergy (CMA) is the most common food allergy among children. An oral food challenge (OFC) remains a mainstay of the diagnosis of CMA, especially for the non-IgE-mediated type; however, this test can be risky and time-consuming. Hence, there is a need to identify biomarkers. Fecal calprotectin (FC) showed variable results, with good reliability and reproducibility in CMA patients. In this prospective study, we enrolled 76 children (aged 5-18 months) with CMA-related gastrointestinal and cutaneous symptoms following guidelines from the European Society of Pediatric Gastroenterology, Hepatology and Nutrition. Clinical assessments included history, physical examination, skin prick tests, and IgE assays. FC levels and the Cow's Milk Related Symptom Score (CoMiSS) were measured in 51 patients pre (T1) and post-diet (T2), with a subgroup analysis of 15 patients with elevated baseline FC (>50 mg/kg). The results showed that FC levels significantly decreased after the elimination diet (median: 30 mg/kg at T1, 16 mg/kg at T2; < 0.01). In the subgroup with higher FC levels, median values dropped from 90 mg/kg to 33 mg/kg ( < 0.01). CoMiSS also improved (median: 8.50 at T1, 3.00 at T2; < 0.01). Linear regression analysis showed no correlation between FC values and the CoMiSS at T1 and T2. In conclusion, the reduction in FC value after an elimination diet suggests that it could be considered a possible biomarker of bowel inflammation in CMA patients. Further studies are necessary to confirm these data and to evaluate and standardize the use of FC for diagnosis and follow-up of CMA.