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Abstract Background Peru is facing a double burden of malnutrition (DBM), characterized by the co-existence of undernutrition and overnutrition. Double-duty actions that concurrently target common drivers of undernutrition and overnutrition, while ensuring no unintended side effects, are recommended to effectively address the DBM. To understand these complex common mechanisms and design context-specific double-duty actions, there is a need for participatory systems approaches. This paper provides a case study of applying a community-based system dynamics approach to capture stakeholder perspectives of food system drivers of the DBM in two regions in Peru. Methods We implemented a multi-stage community-based system dynamics approach, which included processes for research capacity building for systems approaches, and the designing, piloting, and implementation of stakeholder workshops. A total of 36 stakeholders, representing diverse perspectives, participated in five group model building workshops. Stakeholder views are presented in a causal loop diagram that showcases the feedback mechanisms between key food system drivers of overweight and stunting in Peru. Results The causal loop diagram highlights that prioritization of undernutrition over overnutrition in the policymaking process, due to Peru’s historically high levels of undernutrition, may undermine action against the DBM. It also describes potential mechanisms of unintended impacts of undernutrition policies on the DBM in Peru, including impacts related to within-family distribution and quality of food provided through food assistance programs, and unintended impacts due to regional dynamics. Conclusions This paper highlights the importance of a participatory approach to understand local needs and priorities when recommending double-duty actions in Peru and shares practical methodological guidance on applying participatory systems approaches in public health.