A part of scientific knowledge that aims to promote sustainable development consists in management principles of complex systems. Its implementation requires a precise understanding of the situation of action and of the actors’ involvement in the situation. It can no longer be thought of in terms of transfer. Successful implementation relies on changing the ways of understanding and valuing the local context, as well as the actors’ practices. Transdisciplinary approaches are proposed to facilitate mutual learning between researchers and local actors that lead to a better understanding of the action situation. We explore the benefits of such approaches and their implications for those involved in the field of agroecology. Agroecology is based on the implementation of scientific principles that aim to make agriculture more sustainable. These include the creation of agricultural production based on biodiversity. Analysis of three case studies concerning the biodiversification of forage production shows that implementation is not getting farmers involved in the researcher’s project, but rather that researcher’s intentions find a place in the farmer’s projects. Researchers adapt their scientific production to the farmer’s needs while farmers review their goals and means as a result of these interactions. The result is a better understanding of the situation to be transformed by both researchers and farmers. This new insight justifies making implementation an integral part of the scientific approach. However, both researchers and farmers committed to the situation need to be ready to leave their comfort zone.