COVID-19 was declared a pandemic in March 2020 by the WHO (World Health Organization), and by mid-May 2021, it had already affected approximately 164.5 million people, with at least 3.4 million deaths. The pandemic has caused a state of panic across the world, challenging food security, agriculture, and food supply chains as a whole. Research on the analysis of agri-food chains during COVID-19 indicates a greater impact on food chains from local suppliers, especially the shorter chains, which are those with few links. In this context, this work aims to analyze the impacts of COVID-19 on short fresh food chains and identify the best practices to combat the effects of the pandemic. To achieve this goal, we develop a case study in a producer organization in Rio de Janeiro. This study covers a scoping review that identifies the main impacts, practices, policies, and strategies of the pandemic in this supply chain in the literature. Then, the results are empirically evaluated through a survey in the organization to assess whether the variables found in the literature represent its reality. Finally, the problem is modeled through a system dynamics simulation representing the cause-and-effect relationships between the actors in the chain, their impacts, practices, policies, and strategies against COVID-19. The contribution of this research is directed not only to the academy but also to the local community, using tools and techniques from the academy to generate knowledge about the functioning of their system.