This study aimed to investigate the effect of inoculation with Weissella paramesenteroides NCU031042 and Lactiplantibacillus plantarum NCU001980 on the quality of soy sauce. Three inoculation strategies were evaluated, the analysis results of flavor components and biogenic amine (BA) levels suggested that the optimal strategy for soy sauce fermentation was to inoculate W. paramesenteroides NCU031042 on day 1 (1.0 × 10⁶ CFU/g), and L. plantarum NCU001980 on day 7 (1.0 × 10⁶ CFU/g). This enhanced its organic acids (1.47-fold), volatiles (1.29-fold), and free amino acids (1.21-fold) flavors. It demonstrated a superior 2-methoxy-4-vinylphenol production capacity and characteristic flavor components such as lactic acid, 1-octen-3-ol, benzeneacetaldehyde, and glutamic acid were increased by 1.38-, 1.45-, 4.10-, and 1.37-fold, respectively. Besides, the content of BA was reduced by 42.26%, and most of them were positively correlated with their precursors, suggesting that the addition of W. paramesenteroides NCU031042 and L. plantarum NCU001980 inhibited the growth of microorganisms involved in BA synthesis or degraded them. This work provides valuable information for the exploration and industrial application of functional microorganisms in soy sauce fermentation.