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The design of sustainable agroecosystems is crucial to meet contemporary environmental challenges such as biodiversity loss and global change. Ecological knowledge, although expected to be an important component of such an endeavour, is to date mainly used under a problem-solving paradigm. Applying recent design theories, which highlight the differences between innovative design and problem solving, we assess the potential of using ecological knowledge in agroecosystem design in three contrasted French case studies representative of agricultural intensification world-wide. In all cases, a design approach generated unexplored agroecosystem configurations and management alternatives. This analysis highlights that ecological science is critical for designing sustainable social-ecological systems, because it orients the design process by identifying key ecological properties to maintain, while opening the range of management options stakeholders can explore. Synthesis and applications. Participatory design approaches of agroecosystems based on ecological knowledge might be key for planning and change: they allow a diversity of stakeholders to contribute to building solutions, thereby strengthening their sense of ownership and responsibility. Infrastructures in support of participatory design processes, set up in close relation to ecological research centres, have the potential to become new cornerstones of innovation for sustainable social-ecological systems.