Fermented foods are microbial ecosystems in which bacteria and fungi convert raw ingredients into stable, nutritious, and health-promoting products. The composition and activity of these microorganisms determine the biochemical and nutritional profile of the final food. We analyzed 17 fermented foods, each in triplicate, using metaproteomics. This analysis revealed that microbial proteins contribute up to 11% of total protein and 60% of identified proteins. Detailed information on file-naming conventions (database files, MS raw files, and output files), as well as food source suppliers, fermenting microorganisms, peptide loading volumes, and LC-MS gradient lengths, is provided in the table FileAndSampleDescription_PRIDE_submission.csv.