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.