Undernutrition among infants and children retards the physical and cognitive growth and increases susceptibility to infections and diseases. Educational attainment and productivity of children get adversely affected by undernutrition, NFHS (2019–2020) and IIPS (2021) found the prevalence of undernutrition indicators to be high among the under-five children of the nation and tribal children to be in a more vulnerable condition. Mean mid-upper arm circumference (MUAC) is a quick, simple and precise screening tool to use in large-scale community-based nutritional programme. The present study aimed to assess the prevalence of undernutrition based on MUAC among three tribes of three distinct ecological zones of India, namely Bhil Tribe (Desert ecology), Dhodia tribe (Coastal ecology) and Kinnaura tribe (Himalayan ecology). The present cross-sectional study consists of 985 tribal children (509 boys and 476 girls) belonging to the age group 0–1 through 5+ years (below six years). Z-score was computed using WHO (2006) recommended age and sex-specific cutoff points for MUAC and the prevalence of undernutrition was assessed for children of below five years of age. MUAC has been found to have significant age difference among all communities ( p < .001). Prevalence of undernutrition was found to be the highest among the Bhil tribe, the one residing in the desert ecology (41.03%) followed by Dhodia (18.06%) and Kinnaura tribe (12.16%). Among Bhil and Kinnaura children, prevalence of undernutrition was higher among the girls, while the Kinnaura boys manifested higher prevalence of undernutrition in comparison to their counterpart. Significant ( p < .01) sex difference in undernutrition prevalence was found only in case of Bhil tribe (boys: 33.33%, girls: 48.02%). The prevalence of undernutrition significantly differs among the tribes of three distinct ecological zones ( p < .001). The nutritional status of the tribal children, particularly that of the Bhil children, was unsatisfactory. To improve the nutritional wellbeing of the tribal population of the nation, studies at regular intervals focusing on the causes responsible for nutritional status are needed.