Background: The study aimed to investigate the association between daily consumption of coffee or green tea, with and without habitual bread consumption for breakfast, and components and prevalence of metabolic syndrome in Japanese populations. Methods: The study population consisted of 3539 participants (1239 males and 2300 females). Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression analyses to evaluate the associations of daily coffee and green tea consumption with the prevalence of obesity, visceral obesity, and metabolic syndrome. Results: Coffee consumption was associated with significantly lower proportions of visceral obesity (OR: 0.746, CI: 0.588–0.947) and metabolic syndrome (OR: 0.706, CI: 0.565–0.882). On the other hand, green tea was not associated with visceral obesity (OR: 1.105, CI: 0.885–1.380) or metabolic syndrome (OR: 0.980, CI: 0.796–1.206). The combination of daily drinking coffee and eating bread at breakfast time was associated with significantly lower proportions of obesity (OR: 0.613, CI: 0.500–0.751) (p = 0.911 for interaction), visceral obesity (OR: 0.549, CI: 0.425–0.710) (p = 0.991 for interaction), and metabolic syndrome (OR: 0.586, CI: 0.464–0.741) (p = 0.792 for interaction). Conclusion: Coffee consumption was significantly associated with lower visceral adipose tissue and lower proportions of visceral obesity, but the same was not true for green tea consumption. Furthermore, in combination with coffee consumption, the addition of eating bread at breakfast time significantly lowered proportions of visceral obesity and metabolic syndrome, although there was no interaction between coffee and bread.