The inclusion of social actors is widely acknowledged as a precondition for just and sustainable adaptation strategies to climate change. The integration of diverse types of scientific and local knowledge contributes to a better understanding of problems and increases the relevance of science at the local scale. In this study, we - an interdisciplinary team of scientists - employed a transdisciplinary methodology to enable the discussion of collaborative action the Salvadoran coffee sector needs to adapt to current and future impacts of climate change. Through a stakeholder encounter we elicited knowledge exchange among stakeholders to generate (i) a collective awareness of the experiences of climate impacts and (ii) outline a research agenda to facilitate a transdisciplinary climate change adaptation strategy. We used a suite of standard and participatory data-gathering methods, including desk research, in-depth informal conversations, questionnaires, field visits, small-group discussions, and a one-day workshop. In this paper, we present the methodological approach and the outcomes of the transdisciplinary research process. We ultimately outline a collectively generated research agenda using the input of stakeholders who partook in the workshop.