Food supply chain management is a main object of the food security. How to form an effective food supply chain in pandemic conditions is the one of the most important questions nowadays. The agro-food system is becoming not only a tool for solving many economic and social problems that arise in the context of a pandemic, but itself is experiencing a serious impact from consumers, business, and the state. The pandemic negatively affected the agri-food system of different countries. Among the main problems, we will single out the reduction in demand for fresh food, disruptions in the supply of incoming resources, both for the production of products and for their sales, a shortage of labour, especially seasonal. The article examines the impact of the COVID-19 pandemic on the food supply chains in Russia. Using the example of supply chains in St. Petersburg, we show that the food supply chain tends to be shorter because of the consumer's willingness to buy food direct from farmers avoiding risks to be infected with COVID-19. Another change in food supply chain is the increasing role of government in regulation of food security in region.