Meeting the future challenges of the Anthropocene requires designing innovative and sustainable agroecosystems. Ecological knowledge is expected to be an important component of such endeavor. Drawing on recent design theories, we present a study of a French agroecosystems in which we assess the potential of using ecological knowledge in agroecosystem participatory design processes. We show that design processes generate various acceptable agroecosystem configurations and open management alternatives that were not initially identified by researchers. This research highlights that ecological science is critical for designing sustainable agroecosystems, because it orients the design process by identifying key ecological properties that must be maintained, while opening the range of management options stakeholders can explore. Infrastructures supporting participatory design processes, built on to ecology research centers, such as Long Term social-ecological Research sites, could become new cornerstones of technical and governance innovation for sustainable agroecosystems.