Introduction: The postnatal period is important for intestinal microbiota establishment, which is involved with the intestinal development, prevention of pathogens colonization, digestion and synthesis of nutrients, as well as immune and neuronal systems maturation. Intestinal colonization takes place during the first days of life, being influenced by the method of delivery, type of lactation, and the environment. Furthermore, the microbiota composition and functionality might be influenced by maternal and neonatal diet. The objective of this review was to present scientific evidence published during the last years regarding the role of delivery methods, type of lactation, supplementation with pre and probiotics on neonatal intestinal microbiota composition. Methods: In this work, more than 19 articles published during the last 15 years and obtained from different specialized databases (NCBI, Web of Science, Elsevier Journal, Science Direct) are included. We have analysed studies related to humans. Results: The method of delivery and type of lactation might modify the intestinal microbiota in new-borns. Supplementation with probiotics increased the Bifidobacterium and Lactobacillus genera. More studies are needed to evaluate the effects of probiotics in the development and functionality of intestinal microbiota in the newborns. Supplementation with prebiotics may induce the production of secondary metabolites that are able to modulate the newborn epigenome’s. Conclusions: More studies are needed to elucidate the exact mechanisms that modifies in the microbiota composition and describe personalized nutritional strategies to enhance the newborn development.