Diet is a key regulator of microbiome structure and function across the lifespan. Microbial colonization in the first year of life has been actively researched; however, studies during childhood are sparse. Herein, the impact of dietary intake and pre- and probiotic interventions on microbiome composition of healthy infants and children from birth to adolescence is discussed. The microbiome of breastfed infants has lower microbial diversity and richness, higher Proteobacteria, and lower Bacteroidetes and Firmicutes than those formula-fed. As children consume more complex diets, associations between dietary patterns and the microbiota emerge. Like adults, the microbiota of children consuming a Western-style diet is associated with greater Bacteroidaceae and Ruminococcaceae and lower Prevotellaceae. Dietary fibers and pre- or/and probiotics have been tested to modulate the gut microbiota in early life. Human milk oligosaccharides and prebiotics added to infant formula are bifidogenic and decrease pathogens. In children, prebiotics, such as inulin, increase Bifidobacterium abundance and dietary fibers reduce fecal pH and increase alpha diversity and calcium absorption. Probiotics have been administered to the mother during pregnancy and breastfeeding or directly to the infant/child. Findings on maternal probiotic administration on bacterial taxa are inconsistent. When given directly to the infant/child, some changes in individual taxa are observed, but rarely is overall alpha or beta diversity affected. Cesarean-delivered infants appear to benefit to a greater degree than those born vaginally. Infancy and childhood represent an opportunity to beneficially manipulate the microbiome through dietary or prebiotic interventions, which has the potential to affect both short- and long-term health outcomes.