Background: The mode of delivery significantly influences neonatal microbial colonization, with long-term implications for health and disease susceptibility. Vaginal delivery exposes neonates to maternal vaginal and intestinal microbiota, fostering a diverse and beneficial microbial environment crucial for immune development and overall health. In contrast, cesarean section (C-section) bypasses this natural exposure, leading to colonization by skin and environmental microbes, which can result in reduced microbial diversity and increased susceptibility to infections and immune-mediated disorders. This paper examines the impact of delivery methods on neonatal microbial colonization patterns and associated health outcomes. Vaginally delivered neonates acquire beneficial bacteria such as Lactobacillus and Bifidobacterium, which support gut health, immune modulation, and pathogen resistance. In contrast, C-section delivery often results in delayed colonization and an increased prevalence of hospital-acquired bacteria, potentially leading to higher risks of conditions such as asthma, allergies, and metabolic disorders. Interventions such as vaginal seeding and probiotic supplementation offer potential solutions to mitigate the microbial deficits associated with C-sections. Encouraging breastfeeding further enhances microbial diversity and immune function. Policy recommendations should focus on reducing unnecessary C-sections while promoting strategies that support neonatal microbial health. Understanding the relationship between delivery mode and neonatal microbiome development is essential for improving health outcomes. Healthcare providers should consider microbial implications when determining delivery methods to optimize neonatal health.