This paper aims to share and analyze the difficulties and discomfort that social scientists may face when conducting transdisciplinary research. Focusing on the case study of a research project that brought together farmers, farm advisors, social and biotechnical science teachers, and researchers interested in seed management and participatory plant breeding, it questions the use of science and social scientists' position in agroecological transformation processes. The paper provides an analytical insight into the knowledge ecology of stakeholders who want to move away from the hybrid maize varieties bought and grown by farmers in order to work with open-pollinated populations.