Women's empowerment is essential to improve nutrition in low and middle-income countries. We investigated the empowerment of women in agriculture in association with household production and the dietary diversity of children 12–59 months old and their mothers in Timor-Leste. Using the Abbreviated Women's Empowerment in Agriculture Index (A-WEAI) we analyzed 156 dual-adult rural households applying multivariable regression models. We found that the dietary diversity scores of empowered women and their children were higher than among those disempowered. The associations between different measures of empowerment and dietary diversity were larger and more significant among women than children. Food production diversity was consistently associated with children's improved diets. We found small gender gaps in decisions on production, access to resources, and control over income, similar to findings in other Southeast Asian countries. Nutrition-sensitive policies and programmes in Timor-Leste could gain from prioritizing women's empowerment and promoting agriculture diversification strategies as valuable investments to improve the diets and wellbeing of mothers and children.