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The human intestinal flora develops during the first three years of life. Its development is influenced by the maternal diet, the mother’s exposure to antibiotics during pregnancy and breastfeeding, the mode of delivery (vaginal birth or cesarean), the method of feeding (breast milk or infant formula), dietary diversification, exposure to infections, particularly gastrointestinal infections, and the use of proton pump inhibitors and antibiotics. This period is both a window of opportunity and a time of vulnerability, as the intestinal microbiota has limited resilience before the age of three. In cases of dysbiosis, the short-term risk is an overgrowth of pathogenic bacteria, which can lead to gut translocation and sepsis. In the longer term, dysbiosis—together with genetic factors, host immunity, and other exogenous factors—may contribute to the emergence of allergic, inflammatory, and autoimmune diseases. It is therefore important to preserve the intestinal flora by limiting antibiotic use to well-defined indications and, whenever possible, to use narrow-spectrum antibiotics with low gastrointestinal excretion. The development of microbiota-based therapies could play an important role in the future. It remains necessary to continue developing reliable investigative strategies and standardized benchmarks, supported by large cohort studies of newborns and infants, to further our understanding of the mechanisms underlying host–microorganism–environment interactions.