Agroforestry is seen as a promising set of land use practices that can lead to increased ecological integrity and sustainable benefits in mountain areas. Agroforestry practices can also enhance smallholder farmers' resilience in the face of social and ecological change. There is a need for critical examination of existing practices to ensure that agroforestry recommendations for smallholder farmers are socially inclusive and grounded in local experience, knowledge, and perceptions. In this paper, we present a transdisciplinary systems approach to the identification and analysis of suitable agroforestry options, which takes into account gendered perceptions of the benefits and values of natural resources. The 4-step approach consists of an appraisal of local perceptions of the social-ecological context and dynamics, an inventory of existing agroforestry practices and species, a gendered valuation of agroforestry practices and species, and the development of locally adapted and gender-sensitive agroforestry options. In a study using this approach in the Peruvian Andes, data were collected through a combination of participatory tools for gender research and ethnobotanical methods. This paper shares lessons learned and offers recommendations for researchers and practitioners in the field of sustainable mountain development. We discuss methodological considerations in the identification of locally adapted agroforestry options, the understanding of local social-ecological systems, the facilitation of social learning processes, engagement in gender research, and the establishment of ethical research collaborations. The methodology presented here is especially recommended for the exploratory phase of any natural resource management initiative in mountain areas with high environmental and sociocultural variability. © 2016 Mathez-Stiefel et al. This open access article is licensed under a Creative Commons Attribution 4.0 International License.