CONTEXT: Probiotics show promise in preventing and managing food allergies, but the impact of supplementation during pregnancy or infancy on children's allergies and gut microbiota remains unclear. OBJECTIVE: This study aimed to assess the effects of maternal or infant probiotic supplementation on food allergy risk and explore the role of gut microbiota. DATA SOURCES: A systematic search of databases (PubMed, Cochrane Library, Embase, and Medline) identified 37 relevant studies until May 20, 2023. DATA EXTRACTION: Two independent reviewers extracted data, including probiotics intervention details, gut microbiota analysis, and food allergy information. DATA ANALYSIS: Probiotics supplementation during pregnancy and infancy reduced the risk of total food allergy (relative risk [RR], 0.79; 95% CI, 0.63-0.99), cow-milk allergy (RR, 0.51; 95% CI, 0.29-0.88), and egg allergy (RR, 0.57; 95% CI, 0.39-0.84). Infancy-only supplementation lowered cow-milk allergy risk (RR, 0.69; 95% CI, 0.49-0.96), while pregnancy-only had no discernible effect. Benefits were observed with over 2 probiotic species, and a daily increase of 1.8 × 109 colony-forming units during pregnancy and infancy correlated with a 4% reduction in food allergy risk. Children with food allergies had distinct gut microbiota profiles, evolving with age. CONCLUSIONS: Probiotics supplementation during pregnancy and infancy reduces food allergy risk and correlates with age-related changes in gut microbial composition in children. SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration no. CRD42023425988.