Objective To identify the characteristics of the oral microbiota and the relationship of the dental caries and periodontal status in patients aged 0 to 18 years with nonsyndromic cleft lip and palate (CLP).Material and methods A systematic review of the literature was carried out. Five databases were consulted, including publications in English, Spanish and Portuguese. The evaluations of the quality of the observational studies and the experimental studies were carried out with the Newcastle–Ottawa scale and CONSORT guidelines, respectively. The risk of bias of the studies was determined using Rev Manager 5.4, and 5 publications were meta-analyzed.Results In cariogenic microbiota, Lactobacillus spp. and Streptococcus mutans were identified at high levels, and the related periodontopathogenic microorganisms were Prevotella intermedia, Prevotella nigrescens, Porphyromonas gingivalis, Fusobacterium spp., Campylobacter spp., and Fusobacterium nigrescens. The microorganisms found in pre- and postoperative interventions were Staphylococcus aureus, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus pyogenes, Moraxella catarrhalis, methicillin-resistant Staphylococcus aureus and Candida spp., with great heterogeneity in microbiological counts. The meta-analysis revealed that patients with CLP were 2.03 times more likely to have cavities than was the control group (p < 0.005).Conclusion In the microbiota, there was a great diversity of microorganisms that can vary according to the type of fissure and surgical interventions predisposing patients to a greater probability of dental caries.Clinical relevance To study the oral microbiota in CLP that facilitates the progression of dental caries and periodontal disease, take it into account in clinical decision-making and adopt preventive measures to reduce oral comorbidities.