COVID-19 was declared a pandemic in March 2020 by the WHO (World Health Organization), and at the beginning of April 2022, it had infected approximately 490.7 million people, with at least 6.17 million deaths. The pandemic has challenged food security, agriculture, and fresh food chains. Research on the analysis of agri-food supply chains during COVID-19 indicates a more significant impact on small suppliers of these chains, especially the shorter chains, which are those with few links. In this context, this work analyzes the effects of COVID-19 on fresh food chains. Thus, a case study is developed in a producer organization in Rio de Janeiro. This study covers a scoping review that identifies in the literature the main impacts and policies of the pandemic in this chain. Then, the results are evaluated through a survey in the organization to assess whether the variables found in the literature match the variables identified by the survey respondents, who are small producers in the state of Rio de Janeiro. Finally, the problem is modeled through a system dynamics simulation. The results showed that the organization s supply chain is sensitive to impact variables such as increased production cost and non-delivery of products. As increasing production cost and not delivering products, the sales rate is negatively impacted. The investment policy in logistics shows that the sales rate is positively impacted when investment increases.