Few studies have examined the association between coffee consumption and muscle mass; their results are conflicting. Therefore, we examined the association between coffee consumption and low muscle mass prevalence. We also performed an exploratory investigation of the potential effect modification by demographic, health status-related, and physical activity-related covariates. This cross-sectional study included 2085 adults aged 40-87 years. The frequency of coffee consumption was assessed using a self-administered questionnaire. Muscle mass was assessed as appendicular skeletal muscle mass/height2 using a multifrequency bioelectrical impedance analyser. We defined low muscle mass using cut-offs recommended by the Asian Working Group for Sarcopenia. Multivariable-adjusted odds ratios for low muscle mass prevalence were estimated using a logistic regression model. The prevalence of low muscle mass was 5.4% (n = 113). Compared with the lowest coffee consumption group (<1 cup/week), the multivariable-adjusted odds ratios (95% confidence intervals) of low muscle mass prevalence were 0.62 (0.30, 1.29) for 1-3 cups/week, 0.53 (0.29, 0.96) for 4-6 cups/week or 1 cup/day, and 0.28 (0.15, 0.53) for ≥2 cups/day (P for trend <0.001). There were no significant interactions among the various covariates after Bonferroni correction. In conclusion, coffee consumption may be inversely associated with low muscle mass prevalence.