In this paper, we investigate the interplay between labor out-migration, changes in gender roles, and their effects on the maize farming system. The paper unravels these interactions using the data collected from 1053 migrant households in the mountains of Nepal. The result shows that household size positively and the number of 17–60-year-old household members negatively influence maize yield. Remittance income and raising farm animals enhanced maize yield. Geography, especially maize farming in the mountains, showed a reduction (25.6%) in yield. The migrants’ wives stated less maize yield (5%) compared to the other household members. In addition to these contextual factors, women's increased participation in the household chores, rearing and caring of farm animals, and community activities significantly compromised maize yield. However, the remittance income offsets the loss. As women's role in agriculture is central, especially in the context of male labor out-migration, gender-transformative approaches to research and development practices would ensure social justice and equitable benefit sharing. Accounting for their choices and preferences in developing and designing agricultural interventions is thus vital for the long-term sustainability of the mountain farming systems.