Background: Modifiable lifestyle factors and body composition can affect the attainment of peak bone mass during childhood. This study performed a cross-sectional analysis of the determinants of bone health among pre-adolescent Malaysian children with habitually low calcium intakes and vitamin D status in Kuala Lumpur (PREBONE-Kids Study). Methods: Body composition, bone mineral density (BMD), and bone mineral content (BMC) at the lumbar spine (LS) and total body (TB) were assessed using dual-energy X-ray absorptiometry (DXA). Calcium intake was assessed using 1-week diet history, MET (metabolic equivalent of task) score using cPAQ questionnaire, and serum 25(OH) vitamin D using LC-MS/MS. Results: The mean calcium intake was 348.8 ± 180.1 mg/day and mean serum 25-OH vitamin D level was 43.9 ± 14.5nmol/L. In boys, lean mass (LM) was significantly associated with LSBMC (β = 0.539, p<0.001), LSBMD (β=0.607, p<0.001), TBBMC (β=0.675, p<0.001) and TBBMD (β= 0.481, p<0.01). Height was significantly associated with LSBMC (β =0.346, p<0.001) and TBBMC (β =0.282, p<0.001) while fat mass (FM) (β=0.261, p=0.034) and MET score (β =0.163, p=0.026) were significant predictors of TBBMD. Among girls, LM was significantly associated with LSBMC (β = 0.620, p<0.001), LSBMD (β=0.700, p<0.001), TBBMC (β=0.542, p<0.001) and TBBMD (β= 0.747, p<0.001). Calcium intake was a significant predictor of LSBMC (β=0.102, p=0.034), TBBMC (β=0.122, p<0.001) and TBBMD (β=0.196, p=0.002) in girls. Lean mass (LM) was weakly correlated with MET scores (r = 0.205, p = 0.001) but not protein (r = 0.055, p = 0.393) or energy intake (r = 0.101, p = 0.117). MET score (β = 0.207, p = 0.043) was a significant predictor of LM in boys but no factor was found to predict LM in girls. Conclusion: LM is the major determinant of BMC and BMD among pre-adolescent Malaysian children and physical activity is a significant predictor of LM in boys. Encouraging physical activity, calcium intake and optimum diets that build lean body mass should be the focus for developing public health guidance to ensure optimal bone health status during rapid growth.