Re-designing cropping systems to move towards agroecology leads farmers to implement practices which involve biological processes, sometimes qualified as “knowledge-intensive”, as they involve the renewal of agronomic principles and numerous interactions between the systems’ components and their regulations. Agronomists have developed an abundance of models, which encapsulate partial knowledge on systems’ functioning, but these appear to be seldom used by farmers. By contrast, several studies recognize the value of exchanging specific and fundamental knowledge with farmers in relation to technical change processes. This paper discusses how fundamental and generic knowledge acquires an agronomic sense and is reinvested in the action of farmers through their technical changes. We performed an inductive case study of step-by-step cropping system re-design situations. We combined individual interviews with farmers re-designing their cropping-system, and facilitated farmers meeting about a shared technical problem. From full transcripts, we identified each new element of knowledge and its reformulation, its relation to action mentioned by farmers. The focus of our analysis concerns the knowledge which made possible to develop action strategies when farmers were facing hindrances in continuing their technical changes. Our findings concern the specific fundamental knowledge actually mobilized, and the processes of its linkage with action through contextualization. We conclude by suggesting that farmers alternate between systematic and systemic thinking about the biological processes at play in their own situation. This has practical implications for agronomists wishing to support such re-design processes, and provides an insight on how farmers’ experiments might be combined to fundamental scientific knowledge on agroecosystems components to enhance cropping system redesign.