Objective: The South East Asian Nutrition Survey II Indonesia aimed to provide up-to-date data on dietary intake, nutritional and biochemical status of children aged 0·5-12 years in Indonesia 2019-2020. Design: Multistage cluster sampling, stratified by geographical location. Setting: Out of forty-six targeted districts in Indonesia, the study only covered twenty-one districts/cities in Java and Sumatera islands, Indonesia due to COVID-19 pandemic. Participants: A total of 2475 children aged 0·5-12 years were included. Result: The growth (weight-for-age, height-for-age, weight-for-height and BMI-for-age) of Indonesian pre-school- and school-aged children was below the WHO standards. The prevalence of stunting in Java and Sumatera islands was 20·6 and 33·4 % in urban and rural areas, respectively. Stunting was higher in the 1·0-3·9-year age group, boys and rural areas. Overall, 9-12 percent of all children were overweight -obese, with 23·7 % of urban 7-12-year-olds having the highest prevalence. Anaemia was 22·8 % in < 5-year-old and highest in < 1-year-old children. Fe, Zn, vitamins A and D insufficiency was observed in 20·3 %, 11·9 %, 1·9 % and 27·1 % of the children. Dietary intakes of energy, fibre, Ca, Fe, Zn, vitamins A, B1, C and vitamin D below the Indonesian RDA were prevalent and observed in more than half of the children. Conclusion: High stunting, increasing trends of overweight/ obesity, anaemia, serum vitamin D insufficiency, inadequate energy and micronutrient intake in children highlighted the triple burden of malnutrition in Java and Sumatera, Indonesia's most populous regions in 2019-2020, shortly before COVID-19 pandemic era. © The Author(s), 2025. Published by Cambridge University Press on behalf of The Nutrition Society.