The re-design of cropping systems is often seen as a promising form of evolution of these systems for an agroecological transition, and has become the issue of numerous research in Agronomy. These research focuses mainly on the development of possible and satisfactory systems regarding some expected performances, as well as on tools and methods of design and co-design with diverse stakeholders. Less frequent are the studies that analyze what means the re-design as an ongoing process, as a transformation by the farmer of his own activity. In this article, we present contributions from an analysis of these changes in practices, based on interviews and several workshops with farmers and agronomists that accompany them. This analysis aimed in particular at understanding the knowledge generations, circulations, and mobilizations by these actors. We insist on the evolution of knowledge mobilized throughout the change of practice, from which we propose to identify three phases corresponding to specific forms of legitimation of knowledge and specific assessment of the ongoing change by the farmer. Then, we deepen, discussing the implications for agricultural research and development, the link between this dynamic of change and, on the one hand, the indicators used by farmers, whose learning functions are highlighted, and on the other hand, the basic knowledge on biological objects, whose function in building new action strategies is described