Little is known about the relation between the women empowerment in agriculture index, and health and nutrition outcomes among under-five children in Ethiopia. The study's objective was to examine women's empowerment in agriculture and its association with the nutritional status of children (6–59 months) in rural, cash crop producing, and resource-limited settings of Ethiopia. A community-based cross-sectional study was conducted employing 422 households; having women of reproductive age group and children under-five. Stratified simple random sampling was used to identify households; a simple random sampling was used to select villages and households. Women empowerment in agriculture was measured by the abbreviated women empowerment in agriculture index. Even if the overall multi-dimensional five domains of empowerment index (5DE) was not a significant predictor of nutritional status in children (P > 0⋅05), sub-indicators had a pivotal role in child nutritional status. Disempowerment in decisions about input into production [AOR = 8⋅85], empowerment on control of income [AOR = 0⋅35] and availability of livestock [AOR = 0⋅38] were predictors of child stunting, whereas women's disempowerment in production decisions seems beneficiary for wasting, disempowered women have 84 % less likely to have wasted child than empowered women [AOR = 0⋅16]. Dietary and agricultural diversity [particularly livestock farming], and women's empowerment in production decisions were predictors of better nutritional outcomes in children. Therefore, a concentrated effort is needed towards strengthening the multi-dimensional empowerment of women in agriculture emphasising women's input into production decisions, dietary and agricultural diversification, mainly livestock farming.