Recent discussions on the results of food security programs devote key attention to complex interactions between policy interventions and business innovation for improving nutrition outcomes. This shift from linear approaches of food and nutrition security towards a more interlinked and nested analysis of food systems dynamics has profound implications for the design and organization of research and innovation processes. In this article we outline our experience with interdisciplinary and interactive processes of food systems analysis at different scale levels, paying systematic attention to three critical system interfaces: intersections with other systems, interactions within the food system, and incentives for food system innovations (the so-called: 3I approach). We discuss the importance of these interfaces for leveraging food system adaptation and managing food system transformation. We also provide illustrative examples of the relevance of food systems analysis for the identification of appropriate and effective programs for reinforcing the resilience, responsiveness and inclusiveness of novel food and nutrition programs.