Background: The role of muscle fitness in controlling cardiometabolic risk factors during childhood is incompletely understood. Methods: A prospective observational design including 6- to 11-year-old children (n = 512) was used to study associations between 1.5-year changes in handgrip strength, standing vertical jump displacement, the short shuttle run, and a composite of these with changes in composite and single cardiometabolic risk markers. The authors modeled sequential mixed linear regressions controlling for changes in cardiorespiratory fitness, waist circumference, and other putative confounding variables. Results: Statistically significant associations, standardized beta (95% confidence intervals), were observed between changes in composite muscle fitness −0.19 (−0.30 to −0.07), muscular strength −0.15 (−0.25 to −0.06), and agility 0.14 (0.04 to 0.23), but not muscular power −0.06 (−0.14 to 0.03) with changes in the composite risk score. In sex-stratified analysis, associations were robust in girls, but not in boys. Control for changes in cardiorespiratory fitness and waist circumference greatly attenuated associations. Changes in muscle fitness were strongly associated with changes in waist circumference in both girls −0.21 (−0.37 to −0.05) and boys −0.23 (−0.35 to −0.11) after controlling for cardiorespiratory fitness. Conclusions: Our data support a unique role of muscle fitness in the promotion of metabolic health and prevention of excess adipose tissue accumulation in children.