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COVID-19 has caused severe agriculture and food supply chain disruptions; significantly affecting smallholder farmers who supply most of the world’s food; specifically their changes in vulnerability; resilience; and food loss and waste. Therefore; the objective of this study was to understand the complex causal and feedback relationships for this system by developing a dynamic hypothesis and causal loop diagrams utilizing the System Dynamics methodology. Results provide a roadmap for dialogue and a framework for case-specific model development and help to guide policy decisions for smallholder farmers’ survival during health crises.