Bioconversion and fermentation of onion extract by lactic acid bacteria were carried out to enhance the bioavailability of quercetin through the increase of quercetin recovery and aglycone formation. Lactobacillus casei, L. plantarum, and Kluyveromyces lactis were selected as the optimum strains for bioconversion. The environmental conditions to maximize the conversion ratio between glycoconjugate and quercetin aglycone have been evaluated. The concentrations of quercetin after fermentation of onion slurry by K. lactis and L. casei increased to 260% and 318%, respectively; however, the quercetin concentrations decreased after 48 hours of fermentation. Additionally, the quercetin hexose concentration increased to almost 141%. Controlling the initial pH of the onion juice increased the lactic acid production by L. casei and L. plantarum by more than two-fold. Meanwhile, the concentration of quercetin hexose decreased rapidly with the increased production of aglycones. The scale-up experiments showed the same fermentation efficiency; however, thermal sterilization reduced the quercetin glycone concentrations drastically.