The aim of this paper is to assess Czech food consumers’ behavior when buying organic products during the COVID-19 pandemic, with an emphasis on the place of purchase of organic agriculture and food products—especially those purchases with the shortest logistics value chain, i.e., purchase at farmers’ markets, or directly from the producer—and a comparison with the current most common places of purchase of organic products in the Czech Republic, supermarkets and hypermarkets. Categorical data analysis methods were used to create a profile of the consumer according to the most frequent purchase locations. To create mathematical–statistical models and interpretations, the methods of logistic regression, correspondence analysis and contingency table analysis were chosen. According to the results of the survey, respondents under 25 years of age are the least likely to make purchases at farmers’ markets or directly from the producer. Consumers aged 26–35 and with a university degree are the most likely to buy organic agriculture and food products at this location, followed closely by older respondents in the categories 36–45 and 46+ and with a secondary education. It is important for manufacturers to have an overview of where, in what quantities, and for what reasons consumers buy their products, especially for reasons of production optimization and planning, ecological concerns, rural development, and the impact on local areas and the value chain.