Background: Recent studies have reported an association between toothbrushing frequency and systemic health. Plaque control, achieved through frequent brushing, is known to prevent dental caries and periodontal disease, potentially reducing the risk of systemic diseases. However, individuals with good oral health behaviours may also exhibit healthier lifestyle habits which could impact systemic health. In examining the relationship between oral health behaviours and systemic health, it is important to consider the influence of factors that mediate the relationship between them. This study conducted mediation analyses to evaluate the extent to which lifestyle habits and periodontal status mediate the relationship between oral health behaviours and systemic health. Methods: Health examinations, including dental assessments, were performed on 15,579 individuals at the Aichi Health Promotion Foundation. Of these, 12,540 participants aged 40–74 years were included in the analysis. Mediation analyses were conducted using the number of metabolic syndrome (MS) components as the outcome variable, oral health behaviours (regular dental visits, use of interdental brushes or dental floss, and toothbrushing frequency) as exposure variables, lifestyle habits (smoking, drinking, exercise, and eating habits) and periodontal status as mediators, and age and sex as covariates. Results: Regular dental visits showed significant total and indirect effects on MS, although no significant direct effect was observed. The use of interdental brushes or dental floss and toothbrushing frequency demonstrated significant total, direct and indirect effects on MS. Exercise habits, eating habits and periodontal status were significant mediators in the relationship between regular dental visits and MS. These mediators also significantly influenced the associations between both the use of interdental brushes or dental floss and toothbrushing frequency with MS. Conclusion: The relationship between oral health behaviours and MS is mediated by lifestyle habits and periodontal status. Among the mediating variables tested in this study, the indirect effects of diet and exercise habits tended to be stronger than the indirect effect of periodontal disease. Oral health behaviours may influence systemic health through their impact on lifestyle habits. © The Author(s) 2025.