In-depth knowledge of the microbes responsible for biogenic amine (BA) production during soy sauce fermentation remains limited. Herein, the variations in the BA profiles, microbial communities, and microbes involved in BA production during the fermentation of soy sauce through Japanese-type (JP) and Cantonese-type (CP) processes were compared. BA analysis revealed that the three most abundant BA species were putrescine, tyramine, and histamine in the later three stages (1187.68, 785.16, and 193.20 mg/kg on average, respectively). The BA profiles differed significantly, with CP samples containing higher contents of putrescine, tyramine, and histamine (P < 0.05) at the end of fermentation. Metagenomic analysis indicated that BA-producing genes exhibited different abundance profiles, with most genes, including speA, speB, arg, speE, and tyrDC, having higher abundances in microbial communities during the CP process. In total, 15 high-quality metagenome-assembled genomes (MAGs) were retrieved, of which 10 encoded at least one BA production-related gene. Enterococcus faecium (MAG10) and Weissella paramesenteroides (MAG5) might be the major tyramine producers. The metabolic pathways for BA production were predicted. The high putrescine content in CP might be associated with the high abundance of Staphylococcus gallinarum (MAG8). This study provides a comprehensive understanding of the diversity and abundance of genes involved in BA synthesis, especially at the species level, during food fermentation.