In this study, we compared the analytical fingerprint and bioactivity of three onion extracts, including an aqueous, a methanol, and a fermented aqueous extract. The extracts were characterized by HPLC-DAD, LC-MS, and GC-MS analyses. The antibacterial, antigenotoxic, and antiproliferative activity of these extracts was assessed by means of agar disk diffusion, bacterial growth kinetics, a comet assay, cell cycle distribution analysis, and cell viability testing. Both the aqueous and methanolic extracts showed a typical flavonol-fingerprint as assessed by HPLC measurements and showed little to no bioactivity. The fermented aqueous extract, which lacks the usual onion flavonoid profile, was found to be the most active in all of the assays. This finding indicates that metabolites of onion compounds, generated by lactic acid fermentation, may be more active than their precursor substances.