Infants born at high altitudes, such as in the Puno region, typically exhibit higher birthweights than those born at low altitudes; however, the influence of ethnicity on childhood anthropometric patterns in high-altitude settings remains poorly understood. This study aimed to characterise the nutritional status, body composition and indices, and somatotype of Quechua and Aymara children aged 6–10 years. A cross-sectional, descriptive, and comparative design was employed, with a simple random sampling of children from six provinces representative of the Puno region, including 1,289 children of both sexes. Twenty-nine anthropometric measurements were taken, and fat, muscle, and bone components were assessed using bioelectrical impedance analysis. Standardised equations were applied to determine body indices. Among the findings, most children presented normal nutritional status according to BMI-for-age and height-for-age Z-scores. However, high rates of overweight and obesity were observed in Aymara (39%) and Quechua (28.4%) children, with differences in fat content between ethnic groups at the 5th, 10th, 50th, and 75th percentiles. Both groups were characterised by brachytypy and brachybrachial proportions; Quechua children were mesoskelic and Aymara brachyskelic, with macrocormic proportions, rectangular trunks, and broad backs. The predominant somatotype was mesomorphic, with a stronger endomorphic tendency among Aymara. It is concluded that both groups exhibit normal nutritional status; however, Aymara children show a greater tendency towards fat accumulation and notable morphological differences. Differences were also observed in limb proportions, particularly a relatively shorter lower limb.