Purpose: This study aimed to describe the growth, body protein status, and micronutrient biomarkers of Brazilian infants with cow’s milk allergy (CMPA) at baseline and at 18 months of follow-up in comparison with their healthy peers. Methods: Thirty infants with CMPA younger than six months of age were included in this longitudinal study, and their nutritional status was compared with that of 24 non-allergic age-matched children. Anthropometric measurements were used to assess growth, and blood and urine samples were analyzed for protein and micronutrient status. Mixed linear models adjusted for birth weight, socioeconomic status, infant feeding at baseline, weightfor-age, C-reactive protein, serum albumin, micronutrient dietary supplementation, and salt consumption were employed to evaluate the evolution of nutritional parameters throughout the follow-up period. Results: Overall, the mean age of the children at enrolment was 2.9 (standard deviation 1.7) months, and 29 children (53.7%) were male. Infants with CMPA showed a higher prevalence of functional iron depletion (transferrin saturation <20) (p=0.027), lower serum ferritin (p=0.009), and lower urinary iodine (p=0.034) levels than non-allergic children at baseline.Patients with CMPA showed a higher increment in weight-for-age and length-for-age over time than those in the control group (p<0.01). Mixed linear analyses showed a significantly lower increase in serum vitamin B12 (s-B12) (p=0.001) and urinary iodine (p<0.001) concentrations over time compared to the control group. Conclusion Infants with CMPA on a cow’s milk elimination diet had a higher weight and length at 18 months of follow-up but showed signs of inadequate iron, iodine, and B-12 vitamin status.