Our paper highlights questions addressed by ecologization processes in agriculture to agronomic sciences dealing with the study of farmer practices and the design of new farming systems. Since the aim of ecologization is the withdrawal or reduction of the use of inputs or of specific technologies (pesticides, soil tillage) and their substitution by natural processes and natural auxiliaries, we point out the interest for agronomic science to take into account the action of natural entities besides that of farmers. Based on a review of founding texts in agronomy, we highlight the fact that these natural auxiliaries or processes have so far been mainly considered as limiting factors. We also show that the attention paid by agronomists to farmer rationale has tended to minimize attention paid to biological entities and processes and contributed to developing an anthropocentric analysis of production systems. We insist on the fact that the move of agricultural systems toward more environmentally friendly and efficient practices makes it necessary to incorporate them in the set of ‘actors’ involved in the production processes beside farmers and their technical interventions. Our reflection draws on the theoretical proposals of the actor-network theory in sociology, following the symmetry principle which invites to consider in an equal way human and non-human entities in sociotechnical dynamics. We then propose guidelines for reflection, stressing in priority the need for a re-delineation of what may be considered as action and work within the production process. We insist on viewing observation as a form of action and on rethinking arrangements between human inaction and biological processes. We also urge to consider new temporalities and spatiality in the analysis framework, including the long-term properties of bio-ecological dynamics and the integration of cultivated fields in wider ecological spaces.