Poor physical fitness is associated with increased health‐related risks in children. The association of nutritional status indicators and physical fitness in children residing in developing countries is not well characterized. We conducted a cross‐sectional study among 1945 children 5–12 y of age in Bogotá, Colombia, to assess whether anthropometric and micronutrient status indicators were associated with performance in the shuttle run and standing long jump tests. Stunted children scored significantly lower in the run (p=0.0002) and jump (boys only; p=0.003) tests than non‐stunted children. Children who were thin or overweight/obese ran slower than normal weight children (p<0.01). Lower jump scores were associated with overweight/obesity and greater fat arm area in boys only (p<0.0001). Girls with low ferritin concentrations ran slower than children with normal ferritin (p=0.02). Erythrocyte folate concentrations were linearly related with higher run (p<0.0001) and long jump scores (p=0.0001) in both sexes. Boys with marginal or low vitamin B‐12 status had 4 cm lower long jump scores than children with normal status (p=0.01). Sub‐optimal anthropometric and micronutrient status are related to poorer performance in fitness tests. The effects of improving nutritional status on physical fitness of children warrant investigation. Funding: Secretary of Education of Bogotá, DRCLAS at Harvard University, National University of Colombia, National Institute of Health of Colombia, NIH training grant T32DK07703