Fermentation with filamentous fungi is known for the ability to convert bioactive compounds. The aim of this research was to investigate the metabolism of glycosidic derivatives of kaempferol and quercetin during fungal fermentation of extracts from cauliflower outer leaves and onion by Rhizopus oryzae and R. azygosporus. The highest release of kaempferol and quercetin was observed after 2 days and 1 day of fermentation with R. oryzae, respectively. It was proposed that glycosidic compounds were initially deglycosylated to form kaempferol-3-glucoside and quercetin-3-glucoside and then further metabolized into their aglycones. Clear differences in conversion efficiency towards the aglycones were observed between the two Rhizopus strains. Although both flavonoids only differ in one hydroxyl group, the metabolism of the glycosides towards their respective aglycones, kaempferol or quercetin, was different. It is concluded that the fermentation with R. oryzae and R. azygosporus could be considered as a way to produce kaempferol and quercetin aglycone from their glycosidic derivatives.