Current research and innovation (R&I) systems are not equipped to fully serve as catalysts for the urgently needed transformation of food systems. Though research on food systems transformation (first order: ‘what?’) and transformative research (second order: ‘how to’) are rapidly gaining traction in academic and policy environments, current efforts fail to explicitly recognize the systemic nature of the challenges associated with performing transformative second-order research. To recognize these manifold and interlinked challenges embedded in R&I systems, there is a need for a coupled-systems perspective. Transformations are needed in food systems as well as R&I systems (‘how to do the “how to”’). We set out to conceptualize an approach that aims to trigger double transformations by nurturing innovations at the boundaries of R&I systems and food systems that act upon systemic leverage points, so that their multisystem interactions can better support food system transformations. We exemplify this coupled-systems approach by introducing the FIT4FOOD2030 project with its 25 living labs as a promising multilevel boundary innovation at the cross-section of R&I and food systems. We illustrate how this approach paves the way for double systems transformations, and therefore for an R&I system that is fit for future-proofing food systems.