This review explores the intricate relationships between antibiotic use during cesarean section (CS) and its long-term effects on neonatal gut microbiota and subsequent health outcomes. The human microbiome, especially the gut microbiota, is a complex ecosystem that plays a crucial role in health and disease. It is established early in life and is influenced by numerous factors including genetics, diet, lifestyle, and particularly, perinatal antibiotic exposure. The development of the gut microbiota starts before birth, and the mode of delivery significantly impacts its initial composition. Infants delivered by CS exhibit differences in their microbiota, characterized by reduced diversity and lower levels of Bifidobacteria and Bacteroidetes compared to those born via vaginal delivery. This alteration can be attributed to the lack of exposure to the maternal vaginal microbiota and the widespread use of prophylactic antibiotics during CS. These antibiotics cross the placenta and affect the fetal gut microbiome during a critical period of immune and metabolic programming. Studies highlight that early antibiotic exposure is linked to an increased risk of developing conditions such as obesity, asthma, and inflammatory bowel disease later in life.