Agroecology has three practical forms—a scientific discipline, an agricultural practice, and a social movement. Their integration has provided a collective-action mode for contesting the dominant agro-food regime and creating alternatives, especially through a linkage with food sovereignty. At the same time, agroecology has been recently adopted by some actors who also promote conventional agriculture. Agroecology can play different roles—either conforming to the dominant regime, or else helping to transform it—contingent on specific empowerment strategies. Tensions between “conform versus transform” roles can be identified in European agroecological research, especially in three areas: farm-level agroecosystems development; participatory plant breeding; and short food-supply chains remunerating agroecological methods. To play a transformative role, collaborative strategies need to go beyond the linear stereotype whereby scientists “transfer” technology or farmers “apply” scientific research results. To the extent that farmer–scientist alliances co-create and exchange knowledge, such gains can transform the research system.