Demonstrating the clinical consequences of osteosarcopenic obesity (OSO) is complex. This study evaluated clinical manifestations and factors associated with bone and muscle loss in Koreans with obesity. This cross-sectional observational study enrolled Koreans with obesity aged ≥ 50 years from the Korea National Health and Nutrition Examination Survey. Clinical manifestations were compared among four groups: obesity (O), sarcopenic obesity (SO), osteopenic obesity (OO), and OSO. Factors associated with appendicular skeletal muscle mass (ASM) or bone mineral density (BMD) were evaluated. OSO increases with age in both sexes. Men with SO and OSO had increased cardiometabolic diseases and markers, percentages of body fat (BF %), and trunk fat (TF %), and decreased limb fat percentage (LF %). Women with SO and OSO had increased metabolic markers, BF %, and TF % but those with OSO had increased cardiometabolic diseases and lower LF %. Both sexes with OSO had decreased ASM and vitamin D, and higher vitamin D deficiency. BF % was negatively associated with ASM and femur BMD in both sexes. TF % was negatively and LF % was positively associated with ASM in both sexes and with femur BMD in women. Vitamin D was positively associated with femur BMD in men and with ASM and BMD at all sites in women. ASM and BMD were positively associated with each other. Appendicular muscle loss is metabolically significant regardless of bone loss in men; however, appendicular muscle loss with bone loss is metabolically more significant in women. Regional body composition, fat distribution, and vitamin D deficiency were associated with OSO phenotype in both sexes.