Pesticides used in agriculture are a matter of concern regarding the balance between their benefits and drawbacks. Current assessment frameworks, mainly regulatory, do not fully cover the spectrum of effects of their uses. Moreover, these effects are rarely assessed under real-life conditions involving complex systemic interactions that involve different aspects of biodiversity and affect different dimensions of health. A more global approach is necessary to address these issues as well as conditions and consequences of reduction of use, but it comes up against many disciplinary and conceptual barriers. At INRAE, the national research institute for agriculture, food and the environment in France, two internal programmes are proposing to coordinate to initiate a response to this difficulty. The aim is to combine discussions on health related to food systems with those on biodiversity in rural areas. The objective is to develop conceptual frameworks and a shared scientific culture that will provide a solid framework for proposing hypotheses and testing them. This ambitious co-construction will be based on the sharing of acquired knowledge and a multicriteria and cross-questioning approach and integrated modelling strategy that should lead to the establishment of an interdisciplinary research group capable of addressing these issues in their entirety. The presentation outlines these issues and the construction phases of this original approach.