Early microbial colonization plays a foundational role in shaping the infant’s immune, metabolic, and neurological development. The mode of delivery significantly influences this process. Vaginal birth enables physiological exposure to maternal microbiota, while elective cesarean section disrupts this transfer and results in delayed colonization and reduced microbial diversity. This review examines how different delivery modes affect neonatal gut microbiota composition and evaluates their long-term implications for health, with a focus on immune regulation, metabolic programming, allergic conditions, and neurodevelopmental outcomes. Relevant literature from 2010 to 2024 was reviewed using PubMed, Scopus, and Web of Science databases. Human studies comparing elective cesarean section and vaginal delivery were included if they analyzed microbiota profiles and at least one long-term clinical parameter. Out of 245 initially screened articles, 36 were selected based on methodological quality and relevance. Evidence indicates that cesarean section is associated with altered microbial succession patterns that may increase the risk of autoimmune diseases, allergies, obesity, and cognitive or behavioral disturbances. Proposed mechanisms include impaired development of regulatory T cells, reduced production of short-chain fatty acids, and dysregulated immune responses. Although a few studies suggest transient protective effects in specific clinical scenarios, these findings are inconsistent and population-dependent. Supportive interventions such as exclusive breastfeeding and microbiota-based therapies may help restore microbial balance and mitigate adverse outcomes. Future research should focus on identifying biomarkers of dysbiosis and developing personalized strategies to promote microbiota-driven health from birth.