Food Security and Nutrition (FSN) is influenced by diverse and complex factors, and therefore requires a holistic approach to agriculture and food systems plus integration of knowledge from diverse sources in science and society. Using the results of a colloquium held at the University of Hohenheim (Germany) in September 2016 leading up to the recent High Level Panel of Experts (HLPE) Note on Critical and Emerging Issues for Food Security and Nutrition, this article underlines the role of research and innovation as a social and political process and draws attention to neglected types of knowledge. It illustrates the potential of knowledge co-production and co-innovation to transform food systems in order to achieve the Sustainable Development Goals.