Objective This study evaluated the knowledge and practices of pediatricians and nutritionists about cow’s milk protein allergy in infants, with an emphasis on issues related to the exclusion diet and nutritional status. Methods A cross-sectional, descriptive study was performed with a convenience sample of 204 pediatricians and 202 nutritionists randomly invited in scientific events in the city of São Paulo, from November 2014 to March 2016. Results Between 1.5% and 21.0% of respondents indicated inadequate products for the treatment of cow’s milk protein allergy, including goat’s milk, beverages or juices based on soy extract, lactose-free milk formula and partially hydrolyzed formula. The daily calcium recommendation for children between zero and 36 months of age was correctly indicated by 27.0% of pediatricians and 46.0% of nutritionists (p=0.001). Additionally, 96.1% of pediatricians and 82.7% of dietitians (p<0.001) provided guidance on about labels of industrialized products. Conclusion Pediatricians and nutritionists present gaps in knowledge about cow’s milk protein allergy treatment in infants and educational strategies that increase the knowledge of the professionals are important for the management of cow’s milk protein allergy.