Since 2007, the Institute of Social Ecology (SEC) has been conducting socioecological research on the Greek island of Samothraki. Because research is not the only aim, the institute is simultaneously supporting the local population in a process of placing the island on a path towards a sustainable future by “transforming” it into a UNESCO Biosphere Reserve. Based on our research, administrative efforts and networking work, an application signed by the Mayor and unanimously supported by the municipal council has been submitted by the Greek National MAB committee to UNESCO. The application, currently under review, points at including Samothraki in the World Network of Biosphere Reserves. Within this framework, in October 2012, we organized a 1 week student excursion to the island of Samothraki during a crucial phase of the official application process. The objectives of the course were manifold: to (a) expose students to sustainability and development challenges in a local setting seen from the perspective of social ecology, (b) reflect and engage in the design of a management plan to include initial project ideas for the new Biosphere Reserve, such as sustainable tourism, land use, water, waste and energy systems, and (c) allow for the experience of a transdisciplinary research process by learning to interact with stakeholders and conduct interviews in a culturally challenging environment. Methodologically, during the excursion two main approaches were pursued: (a) focus group interviews with local stakeholders (such as fishermen, farmers, local professionals, elderly people in need of care etc.) in order to explore alternative visions for the future of the island and (b) distance sampling methods in order to estimate livestock densities in different area types. This was performed in order to assess the pressing problem of erosion and biodiversity loss due to overgrazing. The aim of the working paper is to provide insight into these methodological approaches and the outcome of research conducted during the course, while reflecting on some of the challenges encountered in this transdisciplinary process and those that might still arise.