This study investigated the associations between biological and environmental factors and gross-motor coordination (GMC) in Peruvian children and adolescents. The sample comprised 7401 boys and girls, aged 6–14 years, recruited from three geographical regions: sea-level, Amazon and high-altitude. Biological variables included age, sex, height, BMI, physical fitness, stunting, and maturational status. Environmental influences included geographical region and school characteristics. Gross-motor coordination was tested with the Körperkoordinationstest für Kinder and the data analyzed by multilevel logistic regression. Results showed a high prevalence of below normal GMC scores. Sex, age, geographical area, biological maturation, BMI (normal versus overweight/obesity), and stunting were all significant predictors of GMC. There was also an interaction between age, sex, and geographical area indicating that older girls who lived at sea-level and high-altitude were more likely to display below normal GMC scores. The school context was less important in predicting GMC problems than the interplay between biological characteristics and geographical region. These results suggest that early identification, as well as educational and pediatric care interventions, are of importance in reducing below normal GMC among Peruvian children and adolescents.