We use a multivariate multilevel model to study the links between physical fitness (PF) and gross motor coordination (GMC) and investigate the influence of predictors affecting their levels across age. We sampled 7918 Peruvians, aged 6-15 years, from sea-level, Amazon region and high-altitude. Composite markers of GMC and PF were derived (GMCz and PFz, respectively). BMI, biological maturation, and stunting were assessed. School characteristics were obtained via an objective audit. School contexts explained 35% of the associations between PFz and GMCz, whereas children's characteristics explained 65% of the total variation. On average, with increasing age, there was a greater increase in GMCz (β = 0.79 ± 0.04, P <.001) than in PFz (β = 0.15 ± 0.03, P <.001); boys outperformed girls (PFz, β = 3.25 ± 0.08, P <.001; GMCz, β = 1.58 ± 0.09, P <.001); those with lower BMI and ahead in their maturation had higher PFz (β = −0.13 ± 0.01, P <.001; β = 1.09 ± 0.05, P <.001, respectively) and GMCz (β = −0.18 ± 0.01, P <.001; β = 0.39 ± 0.06, P <.001, respectively) levels. Stunting was negatively related to PFz (β = −0.30 ± 0.07; P <.001) and GMCz (β = −0.30 ± 0.08, P <.001) and high-altitude Peruvians had significantly lower GMCz (β = −0.93 ± 0.33, P <.001), and those living in the Amazon region had significantly higher PFz (β = 1.21 ± 0.58, P <.001) compared to those living at sea level. A higher number of students was negatively related to PFz (β = −0.016 ± 0.006, P <.001) and positively with GMCz (β = 0.005 ± 0.003, P <.001); the duration of physical education classes was positively associated with PFz (β = 0.70 ± 0.32, P <.001) and GMCz (β = 0.46 ± 0.15, P <.001); and the existence of policies for physical activity was only negatively associated with GMCz (β = −1.17 ± 0.34, P <.001). In conclusion, PFz and GMCz were positively correlated and child- and school-level traits predicted their levels.