The food safety compliance and challenges of microâ€“Food Business Operators (FBOs) that could impact COVID-19 are assessed in this study using the descriptive-comparative research design. The findings reveal that the sanitary conditions of utensils and equipment, the sanitary operations and facilities, the monitoring of time and temperatures, and the maintenance of the sanitary conditions in the facility need major improvement to increase food safety compliance and to contribute in mitigating the transmission of COVID-19. Minor improvements are needed in the handwashing facility, the implementation of the water potability program, Sanitation Standard Operating Procedures, personnel disease control, and hygienic practices. Moreover, the lack of technical knowledge and time to manage and continuously improve food safety system are the challenges experienced by the FBOs. These findings are instrumental to the improvement of the food safety practices, formulation of relevant policies, and conceptualization of research in mitigating COVID-19 relevant to food safety.