Abstract Background Undernutrition is a major public health concern among under-five children in many developing countries. This work evaluated the overall prevalence of under-nutrition by using a composite index of anthropometric failure (CIAF), which helps in the detection of children with multiple anthropometric failures. This research also includes the Spatio-temporal distribution of childhood anthropometric failures across time. Methods Secondary data was obtained from the Ethiopian Demographic and Health Survey for the survey 2005, 2011, and 2016 years. Data included 23,864 samples of children between the ages of 0–59 months, which is a nationally representative sample in Ethiopia. Other than descriptive statistics, the multivariate multilevel logistic regression was used to identify associated factors, and Getis-Ord spatial statistical tools were employed to identify high and low hotspots areas of anthropometric failures. Result The prevalence obtained with CIAF in 2005, 2011, and 2016 was, 53.5 %, 51 %, and 46.2 % of children were suffering from under-nutrition respectively. The spatial analysis revealed areas that are at a higher risk of anthropometric failures consistently were found in northern parts of the country, largely in the Amhara, Tigray, and Afar regions. Multilevel logistic regression analysis showed that the risk of anthropometric failure was higher among older children, had low birth weight, had a mother with low BMI, was in a rural area, had mothers and fathers without formal education. Conclusions In addition to identifying wasted, stunted, and underweight children, CIAF also identified children with multiple conditions, which are often overlooked in nutritional surveys. As revealed by this composite index, the prevalence of anthropometric failure remains considerably high and its spatial distribution also significantly varied across the regions in the country. The established socio-demographic characteristics and districts with a higher risk of anthropometric failure can be used to develop localized intervention and prevention strategies to improve Ethiopian children’s nutritional status and healthcare.