Current societal challenges and recent knowledge acquisition now provide the conditions for the renewal of our collective vision of food science and technology. To meet increasingly complex challenges, it obvious that current reductionist approaches in food science must give way to a knowledge-intensive framework for function-driven research and innovation. This implies a need for more in-depth, multiscale characterization of bioresources, leading to the detailed description of functional entities (molecules, macromolecules, substructures and assemblies etc.) and the development of new transformation technologies. These must provide the underpinning knowledge to devise specific transformations, using minimal energy and water inputs, and generate the targeted end-user products. We should thus consider food manufacturing as a complex systems problem, dealing with heterogeneous product matrices (agents), changing processing conditions (environmental context), non-linear behaviour (phase changes), novel functional properties (emerging phenomena), etc. Accordingly, we propose a new research methodology and innovation agenda, hereby utilizing the knowledge that we have gained in the past decade and described in this Special Issue.