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Plant-based meat analogues (i.e., plant-based meat alternatives or substitutes, or vegan meats) are becoming more and more popular. The quality of the available products is constantly increasing therefore their consumption is also increasing. The primary role of meat analogues is to replace the meat component in meals while appropriate nutrient content and hedonic value will be provided as well. The food safety aspects of these newly emerging food products are less investigated. The aim of this study is to compare the microbial spoilage of identical meals prepared with meat and meat analogues to evaluate the food safety risk of meat analogues. In this work, raw protein materials were tested. Moreover, three pairs of meals prepared with or without meat were microbiologically examined during a storage experiment. Microbial contaminants were low in raw protein sources. In the case of hot meals, the microbial proliferation was faster in samples containing meat analogue, especially if the meals were not cooled. The food safety risk of meals prepared with meat analogues is slightly higher than their meat-containing counterparts, therefore more attention needs to be paid to the preparation, processing, and storage of these foods.