Investigation of the determinants of metabolic outcomes associated with non-communicable diseases is increasingly important in developing countries, but such parameters have not been explored extensively during childhood. The present study assessed the impact of weight gain, measured as BMI-for-age Z-scores, on glucose and insulin concentrations, homeostasis model assessment index of insulin resistance (HOMA-IR) values, and systolic and diastolic blood pressure during school years among Amazonian children. A population-based prospective study of 696 children aged >4 to ≤ 10 years with complete anthropometric information at baseline (51 % females and 86 % of mixed race) was carried out; 411 children had data on metabolic parameters after a median follow-up period of 2·0 years (range 1·7–2·6 years). During follow-up, there was a significant increase in the proportion of overweight children (BMI-for-age Z-score >1) from 10·1 to 15·8 % (P= 0·003). In linear regression models adjusted for the child's sex, age, race/ethnicity, baseline household wealth, birth weight and pubertal development stage, for each unit of BMI-for-age Z-score variation during follow-up, an increase of 8·58 (95 % CI 7·68, 9·60) pmol/l in fasting plasma insulin concentrations and 1·47 (95 % CI 1·30, 1·66) in HOMA-IR values was observed. There was no significant impact of weight gain on glucose concentrations and systolic and diastolic blood pressure. In conclusion, we found evidence that an increase in BMI during a 2-year period affected insulin resistance during school years. Considering the significant increase in overweight in this age group, special attention should be paid to monitoring increases in BMI in children from the Brazilian Amazon.