Objective: 842 million people worldwide are undernourished, while simultaneously the number of overweight and obese individuals increased to 2.1 billion in 2013. There is growing opinion that addressing the global burden of diet-related disease requires a much more comprehensive and multidisciplinary approach than stand-alone public health nutrition interventions such as nutrition education or food labelling. Instead, we need to develop whole of systems interventions to address the core problem and consider the way we grow, process, distribute and commercialize our food. However, there is little evidence or guidance on how to best achieve this goal. This research aims to develop a whole of food systems approach for public health nutrition research by building on systems methods from other fields of science. Specific objectives are to: 1) identify systems methods that are applicable to public health nutrition research; 2) identify how these systems methods and public health research can best be integrated. Methods/results: We explored a range of systems methods which could potentially be applied to public health nutrition research. Based on these, we developed a framework for using and combining different systems methods in public health nutrition research. The framework consists of three main phases: A) availability and affordability of (un)healthy food; B) determinants of (un)healthy food availability and affordability; and C) food system intervention development. Phase A forms the platform of this research combining a series of smaller projects examining food availability, affordability and healthiness. Phase B uses global value chain analysis (GVCA) to identify different attributes of value, including both health and monetary values. Phase C aims to identify sustainable food system public health interventions using Group Model Building (GMB) and logistic modelling approaches. Conclusion: This paper presents why and how systems methods can be used in public health nutrition research. The food system is highly complex and this complexity needs to be acknowledged to find solutions for the current nutrition challenges (obesity, under nutrition), which cannot be solved in isolation. We envision that the methods presented in this paper can form the basis for future research in this area where it can be applied to other public health nutrition research (for example other food products, in relation to specific diseases, different countries) as well as other domains of a sustainable food system not specifically focused on here e.g. economic, social and specific environmental outcomes.