As a highly hydrated gel-type food, soybean curd is perishable and the development of spoilage bacteria has been described. Whole soybean curd (WSC), an innovative soy product retains the most nutrients in raw ingredients and exhibits more nutritive value compared with conventional soybean curd (CSC). However, the risk assessment of WSC is not well evaluated up to now. In this study, the same species of spoilage microorganism were separated from WSC and CSC. Two main spoilage strains were separated and identified as B. subtilis and B. cereus. The risk ranking scores of WSC was higher than that of CSC but still within medium risk range. In summary, we reported the presence of B. subtilis and B. cereus in WSC for the first time. Further, application of the risk ranger tool confirmed that the risk profile of WSC was medium and acceptable.