Objective To investigate the effects of probiotics combined with breastfeeding on intestinal colonization and the risk of allergic diseases in cesarean-delivered newborns. Methods A prospective cohort of 176 cesarean-delivered mothers and newborns admitted to Xinxiang Central Hospital from January 2018 to January 2020 was enrolled, and the newborns were followed for 5 years. According to feeding practice, infants were divided into a breastfed group and a combined group (breastfeeding plus probiotics). Follow-up outcomes were compared between groups. Results Eighty-eight infants were enrolled in each group; 13 were lost to follow-up in the breastfed group and 7 in the combined group. At ages 2, 3, 4, and 5 years, fecal Lactobacillus and Bifidobacterium levels were higher in the combined group than in the breastfed group (P<0.05). Serum immunoglobulin (Ig) A, IgM, and IgG levels were higher in the combined group than in the breastfed group (P<0.05). At ages 3, 4, and 5 years, height and weight were higher in the combined group (P<0.05). The overall incidence of allergic diseases was lower in the combined group than in the breastfed group (P<0.05). At age 5 years, fine motor scores were higher in the combined group (P<0.05). In multivariable logistic regression, the combination of probiotics and breastfeeding was a protective factor for allergic diseases (OR=0.267, P<0.05), whereas family history of allergic diseases was a risk factor (OR=3.611, P<0.05). Conclusions Among cesarean-delivered newborns, the combination of probiotics and breastfeeding positively modulates the gut microbiota, promotes the growth of beneficial bacteria, enhances immunity, and reduces the risk of allergic diseases.