The COVID-19 pandemic has brought impacts on the food system in several ways, such as on the supply and demand of food or changes in consumer preferences. The effects on consumer preferences are directly resulting from changes in people’s daily lives and living conditions. Households challenge income reductions and, in turn, change their food consumption decisions, causing e.g., substitution effects or panic buying behaviour. However, little is known yet about the magnitude of these effects but needs to be analysed to define actions and policies for crisis mitigation and achieving food system resilience and food security. In this study, we estimate the effect of the COVID-19 lockdown on changes in food consumer preferences in Colombia, applying a logit model approach for seven attributes, namely animal welfare, environmental sustainability, information on the origin and manufacturing of food, food appearance, food price, fair payment to the producer, and food packaging. In addition, we provide an analysis of changes in beef consumption during the lockdown since the beef industry is among Colombia’s most important agricultural activities and is heavily affected by substitution effects. Data was obtained in July 2020 during the peak of the COVID-19 lockdown in Colombia, through a virtual survey with 581 food consumers in the four major cities Bogotá, Medellín, Cali, and Barranquilla. Our results show that consumer beliefs regarding these attributes remained mostly stable, but that income is a determining factor for the decision to consume certain types of food, such as beef, rather than for possible changes in beliefs. This means that income ends up being decisive for the consumption of food such as beef and that, for its part, it does not have a greater weight in the change of beliefs of the people surveyed. The results will help the food system actors in defining interventions for achieving food security and resilience.