Obesity is a global epidemic affecting all age groups, populations and income levels across continents. The causes of obesity are complex and are routed in health behaviours, environmental factors, government policy and the cultural and built environment. Consequently, a Whole System Approach (WSA) which considers the many causes of obesity and shifts the focus away from individuals as points of intervention and puts an emphasis on understanding and improving the system in which people live in is required. This protocol describes a programme of research that will: critically evaluate the evidence for WSAs; assess longitudinally the implementation of a WSA to diet and healthy weight to explore the range of levers (drivers) and opportunities to influence relevant partnerships and interventions to target obesity in East Scotland. The programme consists of four workstreams within a mixed methods framework: 1) Systematic review of reviews of WSAs to diet and healthy weight; 2) Longitudinal qualitative process evaluation of implementing two WSAs in Scotland; 3) Quantitative and Qualitative momentary analysis evaluation of a WSA; and 4) the application of System Dynamics Modelling (SDM) methodology to two council areas in Scotland. A Public Involvement in Research group (PIRg) have informed each stage of the research process. The research programme’s breadth and its novel nature, mean that it will provide valuable findings for the increasing numbers who commission, deliver, support and evaluate WSAs to diet and healthy weight nationally and internationally.