Soybean paste was a traditional fermented product in northeast China, mainly fermented by molds, yeast, Bacillus, and lactic acid bacteria. In this study, the safety and fermentation ability of lactic acid bacteria and yeast strains isolated from traditional soybean paste in northeast China were evaluated, and the dynamic changes of biogenic amines, aflatoxin, total acids, amino acid nitrogen, and volatile compounds were investigated during the fermentation of the traditional soybean paste. Among the tested strains, Lactiplantibacillus plantarum DPUL‐J8 could decompose putrescine by 100%, and no biogenic amine was produced by Pichia kudriavzevii DPUY‐J8. Lactiplantibacillus plantarum DPUL‐J8 and P. kudriavzevii DPUY‐J8 with strong biogenic amine degrading capacities were inoculated into the soybean paste. After 30 days of fermentation, the content of biogenic amines and aflatoxin in the fermented soybean paste declined by more than 60% and 50%, respectively. At the same time, compared with the control group without inoculation, the contents of total acid (1.29 ± 0.05 g/100 g), amino acid nitrogen (0.82 ± 0.01 g/100 g), and volatile compounds in soybean paste fermented by L. plantarum DPUL‐J8 and P. kudriavzevii DPUY‐J8 were significantly increased, which had a good flavor. These results indicated that the use of L. plantarum DPUL‐J8 and P. kudriavzevii DPUY‐J8 as starter cultures for soybean paste might be a good strategy to improve the safety and flavor of traditional Chinese soybean paste.