Whereas many studies adopting a broad perspective on sustainability have highlighted the differences and interactions between alternative and conventional models of agricultural production, very few have investigated the contradictions internal to farm organizations engaged in agroecological transition. In order to understand the difficulties faced by farmers in combining multiple aspirations, we study agroecological production cooperatives (APCs) through the tensions between their different institutional logics. We use a qualitative analysis to address these tensions, and the responses to them, related to their territorial, self-management, and agroecological logics. Various local actors have different conceptions of agroecology, based on diverse levels of knowledge of agricultural practices and on dissimilar interests. This entails various preferences regarding technical choices and farm management. Agroecology's emphasis on diversity, local resources, experimentation, labour intensity and the long run may contradict financial considerations and the quality of working conditions of farmers. Setting up deliberation arenas is key to elaborating agreed compromises regarding the agroecological conception, as well as the governance of farm organizations.