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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has recently been demonstrated as a rapid and reliable method for identifying bacteria in colonies grown on culture plates. Rapid identification of food spoilage bacteria is important for ensuring the quality and safety of food. To shorten the time of analysis, several researchers have proposed the direct MALDI-TOF MS technique for identification of bacteria in clinical samples such as urine and positive blood cultures. In this study, processed soybean products (total 26 test samples) were initially conducted a culture enrichment step and bacterial cells were separated from interfering components. Harvested bacterial cells were determined by MALDI-TOF MS and 16S rRNA gene sequencing method. Six processed soybean products (23%) were increased bacterial cells after culture enrichment step and they were successfully obtained the accurate identification results by MALDI-TOF MS-based method without colony formation.