To understand the microbial differences in traditional and industrial production of Northeast soybean paste and identify potential risk microorganisms, this study analyzed the microbial communities in Northeast soybean paste that are produced traditionally and commercially. The bacterial 16S rDNA V3-V4 region (338F/806R) and fungal ITS1 region (ITS1F/ITS2R) were amplified and sequenced using Illumina PE300 sequencer followed by bioinformatics analysis. The results revealed that in the traditionally produced soybean paste, the abundance of bacteria such as Lactobacillus, Tetragenococcus, and Bacillus, and fungi such as Aspergillus, Penicillium, Candida, and Trichosporon were relatively high. Among these, potential risk microorganisms such as Enterobacteriaceae and Staphylococcus were present. There were significant differences in the abundance of high-abundance bacteria like Leuconostoc and fungi like Sterigmatomyces and Fusarium between different soybean pastes that are family-produced. In commercially produced soybean paste, the high-abundance bacteria were Lactobacillus, while the predominant fungus was Aspergillus, albeit with a less diverse microbiota. The differences in microbial community and metabolic functions between traditional and commercial production processes were evident. Functional prediction analysis using PICRUSt2 revealed that traditional soybean paste had higher gene expressions in functions related to glycolysis, gluconeogenesis, glycerol metabolism, organic acid conversion, protein phosphorylation, purine metabolism, and acetaldehyde acid cycle. In contrast, commercial soybean pastes showed higher expressions in protein degradation and amino acid metabolism, which explains why traditional soybean paste has a better flavor, while industrial soybean paste has more stable flavor and shorter production cycle. Comparison with a self-constructed full-length 16S rDNA gene database of pathogens revealed that the biosafety of commercially produced soybean paste is better, while traditional soybean paste may contain more pathogens such as Vibrio vulnificus, Staphylococcus aureus, and Clostridium perfringens. This indicates that during the fermentation of traditional soybean paste, there may be a risk of insufficient control for anaerobic environment, raw material, or hygiene level in the processing stages, leading to the proliferation of toxin-producing strains. Commercial production have a significant advantage in controlling potential risk bacteria. This study provides scientific evidence for optimizing soybean paste production processes, improving product quality, and ensuring food safety.