Malnutrition is responsible for over one-third of deaths among children under the age of five in low-and middle-income countries, including Ethiopia, and is largely preventable. The objective of this study was to determine the prevalence of undernutrition and its contributing factors among children aged 6–59 months in the Gedio zone of Southern Ethiopia. A community-based cross-sectional study design was used, and data were collected from 403 children and their mothers selected through random sampling technique. Anthropometric measures were converted to Z-scores using WHO-Anthro version 3.2.2 software. The prevalence of underweight, wasting, and stunting were 19.7% (95% CI 16-24%), 10% (95% CI 7–13%), and 49% (95% CI 44–54%) respectively. Low birth weight (AOR = 2.8, 95% CI (1.585–4.895), feeding non-diversified diet (AOR = 1.9, 95% CI (1.036–3.497), and being unvaccinated (AOR: 2.0; 95%CI (1.013–4.197) were significantly associated with being underweight. Family size of ≥ 5 (AOR = 4.4, CI (1.274–5.059), meal frequency of < 3 times per a day (AOR = 2.3, CI (1.037–5.024), and index birth interval of < 24 months (AOR = 2.2, CI (1.015–4.843) were significantly associated with wasting. Similarly, children aged ≥ 24 months (AOR = 2.8, CI (1.769–4.474), feeding non-diversified diet (AOR = 1.8, CI (1.153–2.894), total duration of breast-feeding < 12 months (AOR = 4.0, CI (2.547–6.429), and mothers BMI below 18.5 (AOR = 2.2, CI (1.328–3.718) were identified as a predictors of stunting. The study revealed significant levels of undernutrition, including underweight, wasting, and stunting, among children in the study area. Factors such as birth weight, dietary diversity score, and vaccine status were found to be strongly linked to underweight. Additionally, living in a large family, meal frequency, and birth interval were significantly associated with wasting. The age of the child, duration of breastfeeding, dietary diversity score, and maternal BMI status were also significantly linked to stunting. To address this issue, the study recommends promoting healthier feeding practices, dietary diversification, optimal breastfeeding, complete vaccination, wider birth intervals, and improving maternal nutrition to reduce undernutrition among children aged 6–59 months in the area. Implementing these measures could significantly improve the health of children in the study area.