Agricultural intensification tends to maximize provisioning services at the expense of regulating, cultural and supporting ecosystem services (ES). Enhancing agroecosystem sustainability requires both individual and collective solutions, but these are particularly difficult to design and implement since knowledge is lacking and ES may be considered either as private, common or public goods. This study focuses on the role that research can play in such complex design processes. It draws on the reflexive analysis of a place-based and long-term research programme conducted in a Long-Term Social-Ecological Research (LTSER) infrastructure, the Zone Atelier Plaine & Val de S`evre (western France). In this programme, researchers explored several pathways of collaboration with local stakeholders to both produce knowledge and design solutions for sustainable ES management. Four major steps in the research programme are highlighted: (i) a centralized landscape management strategy to reconcile agricultural production and biodiversity; (ii) a participatory design approach to design sustainable agroecosystems; (iii) the implementation of social-ecological experiments on farms to reduce the use of chemical inputs; and (iv) a multifaceted intervention research project to involve a diversity of stakeholders in designing sustainable agrifood systems. For each of these steps, we describe the targeted issues, the ES at stake, the scientific concepts, theories and protocols used, and the design processes and types of interactions developed with stakeholders. We draw lessons from each step, underlining the achievements and difficulties. The paper concludes with insights on the role that researchers can play to foster the collective design of a social-ecological system delivering multiple ES.