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 (GMC(z) 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 GMC(z), whereas children's characteristics explained 65% of the total variation. On average, with increasing age, there was a greater increase in GMC(z) (beta = 0.79 +/- 0.04, P < .001) than in PFz (beta = 0.15 +/- 0.03, P < .001); boys outperformed girls (PFz, beta = 3.25 +/- 0.08, P < .001; GMC(z), beta = 1.58 +/- 0.09, P < .001); those with lower BMI and ahead in their maturation had higher PFz (beta = -0.13 +/- 0.01, P < .001; beta = 1.09 +/- 0.05, P < .001, respectively) and GMC(z) (beta = -0.18 +/- 0.01, P < .001; beta = 0.39 +/- 0.06, P < .001, respectively) levels. Stunting was negatively related to PFz (beta = -0.30 +/- 0.07; P < .001) and GMC(z) (beta = -0.30 +/- 0.08, P < .001) and high-altitude Peruvians had significantly lower GMC(z) (beta = -0.93 +/- 0.33, P < .001), and those living in the Amazon region had significantly higher PFz (beta = 1.21 +/- 0.58, P < .001) compared to those living at sea level. A higher number of students was negatively related to PFz (beta = -0.016 +/- 0.006, P < .001) and positively with GMC(z) (beta = 0.005 +/- 0.003, P < .001); the duration of physical education classes was positively associated with PFz (beta = 0.70 +/- 0.32, P < .001) and GMC(z) (beta = 0.46 +/- 0.15, P < .001); and the existence of policies for physical activity was only negatively associated with GMC(z) (beta = -1.17 +/- 0.34, P < .001). In conclusion, PFz and GMC(z) were positively correlated and child- and school-level traits predicted their levels.