Infancy and toddlerhood are critical phases of life, as the gut microbiota is established here, which influences current and future health. During this period, the microbiota was relatively less stable and highly responsive to environmental factors. Therefore, it is important to understand how dietary factors affect this complex stage of microbial assembly. The effect of feeding practices (breast milk/formula) on microbial colonization in early infancy has been actively studied; however, studies on the effect of diet on the gut microbiota during the complementary feeding period are sparse. The introduction of complementary foods provides abundant new dietary compounds for the gut microbiota, which induces a shift in gut microbiota and metabolism from milk-adapted toward a more mature and diverse adult-like community. Herein, we discuss the impact of dietary nutrients (carbohydrates, proteins, fats, vitamins, and minerals) on microbiome of infants and toddlers. Furthermore, this review summarizes the effects of complementary feeding patterns, specific foods (such as cereals; legumes and nuts; vegetables and fruits; meats; dairy products), food additives, and malnutrition (undernutrition or overnutrition) on gut microbiota of this populations. These findings might deepen our comprehension of the complex interactions between diets and the development and establishment of the gut microbiota. This may facilitate the tailoring of interventions aimed at promoting beneficial modifications within the gut microbial community. Furthermore, the insights gained could inform the design and implementation of safe and efficacious complementary feeding practices.