This study was performed to investigate the changes in microbial communities and metabolites during the long-term fermentation of commercially manufactured anchovy sauce. Samples of commercial anchovy sauce were collected from large-scale fermentation tanks with fermentation periods of up to 7.87 years. The complex bacterial community was simplified to two genera, Tetragenococcus and Halanaerobium, after approximately 0.55 years of fermentation. Although genera, such as Saccharomyces, Cladosporium, Candida, and Aspergillus, were relatively dominant, no clear pattern was identified in fungal community analysis. The longitudinal metabolite profile demonstrated that approximately half (55.8%) of the metabolites present in anchovy sauce were produced within a year of fermentation due to rapid fermentation. Despite the static microbial community, the contents of several metabolites including amino acids and biogenic amines changed continuously during the long-term fermentation of anchovy sauce. This study provides novel insights into the changes in microbiota and metabolites in fish sauce produced without any starter inoculation.