Food allergies are on the rise globally, with cow’s milk allergy being one of the most common allergies in infants and young children. The development of the gut microbiome from birth through to childhood is critical to establish a healthy symbiosis, since this is the period in which infants encounter external stimuli for the first time and the body is trained to respond to these. Human milk is the reference, effectively shaping the infant microbiome, which is associated with optimal immune maturation and protection against infections and potentially also allergy. In this thesis, we show that specific prebiotic and synbiotic (prebiotic + probiotic) ingredients can modulate the microbiota closer to that of breastfed infants leading to clinical benefits related to infection and allergy. The results presented show the potential of these dietary strategies to modulate the gut microbiota in a manner that may be beneficial for a healthy immune development.