Ensuring the food and nutrition security of populations is the basis for sustainable national development and regional stability. In rural Timor-Leste, the majority of people are semi-subsistence farmers who raise livestock, yet diets consistently lack protein and child malnutrition is high. This longitudinal mixed-methods study aimed to examine gender relations, particularly women’s agency, related to livestock production, sale and consumption among smallholders in Timor-Leste. Data collected in two districts over a 12 month period included seasonal livestock herd size, and an adapted Abbreviated Women’s Empowerment in Agriculture Index administered to mothers and male adults in dual-headed households (n=282). Semi-structured interviews (n=35) explored social norms on household decision-making. Seasonal child and maternal dietary diversity and animal-source foods (ASF) intake quantified their dietary quality. Most women and men considered livestock as household assets and made decisions jointly. Yet women showed lower levels of input into decision-making compared to men. Mothers had more autonomy to sell eggs and chickens than larger animals. Despite women frequently reported as the sole decision-makers for small ASF purchases, the qualitative results suggest a greater disparity in control over household resources than indicated by the quantitative data. No differences in ASF allocation according to gender were identified. Seasonality influenced ASF intake, with eggs usually prioritised to children. Women display stronger agency in small livestock management despite unequal bargaining power informed by traditional gender norms. Findings suggest that programs focusing on poultry and pigs have potential to support nutrition outcomes and women’s empowerment, while contributing to poverty alleviation efforts.