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The introduction of modern bioenergy alternatives is promoted to address water–energy–food (WEF) security in the rural highlands of Ethiopia. While the role of women in WEF security is an essential component of these challenges, gender dimensions remain invisible in the nexus debate. This study explores the impact of gender-specific roles between female- and male-headed households on the nexus resources in the rural highlands of Ethiopia using an agent-based modeling approach. This includes capturing the gender-specific responses to modern bioenergy interventions to address current energy crises that may reduce or enhance synergies among nexus resources and whether the introduction of modern bioenergy technology would improve the quality of life for both men and women. Using the participatory gendered mental model of the food–energy–land nexus, a base ABM was developed to simulate the predicted effects under scenarios of population growth and labor reallocation. Initial simulation results show that there is low adoption of alternative bioenergy (i.e., biogas digesters), and the majority remain dependent on traditional energy sources (e.g., fuel wood and animal dung), suggesting further land degradation. Female-headed households that adopt biogas increase their burden of collecting water needed for the operation. Reallocation of labor from crop production to fuelwood collection would result in the reduction of crop yields. It is expected that male-headed households have better crop yields than female counterparts due to gender-specific roles. However, by shifting 10% of labor allocated from energy collection to crop production, yields (i.e., teff and wheat) produced by female-headed households would be comparable to their male counterparts, enhancing their food security. However, the reduced workloads for women resulting from the adoption of biogas digesters will not necessarily enhance their quality of life. This study suggests that trade-offs may arise between efficiency (in resource use) and social equity, which deserve to be further analyzed.