A juvenile’s dependency on their caregiver is significant to the overall development of nutritionally related pathological lesions. However, not all skeletal pathology is caused by nutritional stress; despite anemia being the usual inferred cause, the origin of Cribra Orbitalia (CO) – lesions on the orbital roofs of the cranium– is undetermined. The purpose of this research is to compare the reconstructed diets of juveniles with and without CO and explore connections to dietary patterns (inferred from stable isotope ratios of carbon and nitrogen). Rib bone samples of 79 juveniles with and without CO were sampled from the Kuelap archaeological site in Chachapoyas, Peru (AD 800–1532) – known for its archaeological diversity. Stable isotope analysis was conducted (δ13C and δ15N values) to statistically analyze each group’s values. Samples were further subdivided into age cohorts of infants (0–3 years), juveniles (4–11 years), and adolescents (12–18 years). The diets of juveniles with and without CO were determined to have no statistically significant difference between each other. However, a significant statistical difference did exist between the diets of the different juvenile age cohorts regardless of CO status, indicating that weaning and early dietary transitions through childhood affected the juvenile’s nutritional regime in the region. The research presented is the first study of the relationship between nutrition and CO from Kuelap; significantly, it further explores the lifestyle of past individuals in Chachapoyas through the understanding of childhood diets.