In this work, the effect of solid-substrate fermentation with Aspergillus oryzae, Rhizopus oryzae and Bacillus subtilis of soybean seeds on bioactive phenolic compounds was studied. Among the analysed sample extracts several phenolic compounds, hydroxybenzoics, hydroxycinnamics and flavonoids, such as flavonols, flavanones, isoflavones were identified by HPLC-DAD-ESI/MS. The results obtained indicate that fermentation process carried out in seeds inoculated with different microorganisms produced significant changes in flavonoids and phenolic acids contents. A significant increase in the content of phenolic acids was observed in the samples fermented with the different microorganisms with respect to soybean without fermentation and fermented naturally. Fermentation process produced also important changes in flavonoids compounds, with a significant formation in isoflavone aglycone contents such as daidzein, glycitein and genistein as a consequence of glucosidase activity of microorganism in this process, showing significant differences (p