The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses . Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination . The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans . Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses . Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes . No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date . However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination . On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods . This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next generation sequencing platforms . Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.