The CO-CREATE project aimed to work with young people to create, inform, and disseminate obesity-preventive evidence-based policies using a complex systems perspective. This paper draws lessons from this experience and proposes a protocol for embedding systems thinking within a research project. We first draw on existing systems thinking frameworks to analyze how systems thinking was translated across CO-CREATE, including the flow and relationship between the work packages and in the methods used. We then take the lessons from CO-CREATE and the principles of existing systems thinking frameworks-which focus on various points of intervention planning and delivery but not on research projects as a whole-to formulate a protocol for embedding systems thinking across a research project. Key lessons for future planning and delivery of systems-oriented research projects include incorporating "boundary critique" by capturing key stakeholder (adolescent) values and concerns; working to avoid social exclusion; ensuring methodological pluralism to allow for reflection and responsiveness (with methods ranging from group model building, Photovoice, and small group engagement); getting policy recipients to shape key questions by understanding their views on the critical drivers of obesity early on in the project; and providing opportunity for intraproject reflection along the way.