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Objective: To assess the nutritional status, growth parameters and lifestyle behaviours of children between 0·5 and 12 years in nationally representative samples in Malaysia, Indonesia, Thailand and Vietnam., Design: A cross-sectional study was conducted in the four countries, between May 2019 and April 2021. Data collected can be categorised into four categories: (1) Growth - anthropometry, body composition, development disorder, (2) nutrient intake and dietary habits - 24-h dietary recall, child food habits, breast-feeding and complementary feeding, (3) socio-economic status - food insecurity and child health status/environmental and (4) lifestyle behaviours - physical activity patterns, fitness, sunlight exposure, sleep patterns, body image and behavioural problems. Blood samples were also collected for biochemical and metabolomic analyses. With the pandemic emerging during the study, a COVID-19 questionnaire was developed and implemented., Setting: Both rural and urban areas in Malaysia, Indonesia, Thailand and Vietnam., Participants: Children who were well, with no physical disability or serious infections/injuries and between the age of 0·5 and 12 years old, were recruited., Results: The South East Asian Nutrition Surveys II recruited 13 933 children. Depending on the country, data collection from children was conducted in schools and commune health centres, or temples, or sub-district administrative organisations., Conclusions: The results will provide up-to-date insights into nutritional status and lifestyle behaviours of children in the four countries. Subsequently, these data will facilitate exploration of potential gaps in dietary intake among Southeast Asian children and enable local authorities to plan future nutrition and lifestyle intervention strategies.