Background: Malnutrition has been identified as a factor in growth and learning. The current study aimed to determine the nutritional status and basic learning skills of children from Chocó, Colombia. Methods: We conducted a cross-sectional study of 631 children aged 5–11 years from two schools, collecting anthropometric measurements, nutritional quality surveys and sociodemographic data. Neuropsychological batteries were applied. Results: A total of 523 children were evaluated, with an average age of 8.49 ± 2.1 years. The results revealed that 2.9% of children were underweight, 0.4% were severely underweight, and 4.8% were diagnosed as having stunted growth. In addition, 71.8% of children were unable to draw a human figure. Beery-Buktenica Visual-Motor Integration test (VMI) performance was below the scores expected for these age groups in 73.9% of children. Battery of Differential and General Abilities (BADYG) performance revealed limited verbal skills. In a subsample of 117 children, anemia was detected in 12.8% of cases, and iron deficiency was present in 44.4% of cases. Global malnutrition was associated with impairments in BADYG performance (OR: 1.98; 95% CI: 1.07–3.86). Conclusions: The current results revealed that learning performance was below the expected level for children in these age groups across all of the applied tests. Although malnutrition could partially explain the poor performance of children in tests of learning abilities, additional factors are likely to be involved.