Background: There is still little understanding of the associations between physical fitness variables and bone health in children taking into account key confounders. Aim: The aim of this study was to analyze the associations between performance in tests of speed, agility, and musculoskeletal fitness (power of the upper and lower limbs) with bone mass of different regions in children, considering the adjustment to maturity-offset, lean percentage, and sex. Methods: Cross-sectional study design: the sample consisted of 160 children aged 6–11 years. The physical fitness variables tested were 1) speed, assessed with the running test at a maximum speed of 20 m; 2) agility, assessed through the 4×4-m square test; 3) lower limb power, assessed using the standing long jump test, and 4) upper limb power, assessed using the 2-kg medicine ball throw test. Areal bone mineral density (aBMD) was obtained from the analysis of body composition by dualenergy X-ray absorptiometry (DXA). Simple and multiple linear regression models were performed using the SPSS software. Results: In the crude regression analyses, the results indicated a linear relationship between all the physical fitness variables and aBMD in all body segments, but maturity-offset, sex, and lean mass percentage seemed to have an effect on these relationships. Except for the upper limb power, the other physical capacities (speed, agility, and lower limb power) were associated with aBMD in at least three body regions in the adjusted analyses. These associations occurred in the spine, hip, and leg regions, and the aBMD of the legs presented the best association magnitude (R2 ). Conclusion: There is a significant association between speed, agility, and musculoskeletal fitness, specifically the lower limb power and aBMD. That is, the aBMD is a good indicator of the relationship between fitness and bone mass in children, but it is essential to consider specific fitness variables and skeletal regions