Gender is seminal to agrobiodiversity management, and inequities are likely to be exacerbated under a changing climate. Using in-depth interviews with farmers and officials from government and non-government organizations in Nepal, we explore how gender relations are influenced by wider socio-economic changes, and how alterations in gender relations shape responses to climate change. Combining feminist political ecology and critical social-ecological systems thinking, we analyze how gender and adaptation interact as households abandon certain crops, adopt high-yielding varieties and shift to cash crops. We argue that the prevailing development paradigm reinforces inequitable gender structures in agrobiodiversity management, undermining adaptation to the changing climate.