Dietary protein has a mixed effect on skeletal health and the effect may differ by amount or source of protein. The purpose of this study was to investigate dietary protein in relation to bone density and fat-free mass in rural Korean residents consuming relatively low protein diets. Between 2008 and 2010, 3,330 participants were recruited for a baseline examination of a community-based study in Kangwha. Of those, 1,182 men and 1,393 postmenopausal women were eligible for the present study. Diet was assessed using a food-frequency questionnaire developed for Korean adults. Calcaneal bone density measured by ultrasound was expressed as the stiffness index (SI). Fat-free mass index (FFMI) was defined as fat-free mass in kilograms divided by the height in meters squared. The mean ages of men and women were 59.5 and 60.0 years, respectively. The median daily intakes of total and meat protein were 52.3 and 6.7 g in men and 45.0 and 3.0 g in women, respectively. After controlling for potential confounders, SI and FFMI showed an increasing trend with a higher meat protein intake in men (P for trend = 0.017 and 0.033, respectively), but not in women. No positive association was observed for other food sources of protein. In conclusion, our findings suggest that meat protein contributes to skeletal health in men consuming relatively low protein diets.