A catalytic system for deglycosylation of isoflavone in black soybean milk was established. β-Glucosidase which was covalently immobilized onto the glass microspheres exhibited a significant efficiency for the conversion of pNPG to p-nitrophenol over other carriers. The optimum temperature for pNPG hydrolysis was 40 °C, and complete reaction can be reached in 30 min. Operational reusability was confirmed for more than 40 batch reactions. Moreover, the storage stability verification demonstrated that the glass microsphere catalytic system was capable of sustaining its highest catalytic activity for 40 days. The kinetic parameters, including rate constant (K) at which isoflavone glycosides deglycosylation were determined, the time (τ(50)) in which 50% of isoflavone glycosides deglycosylation was reached, and the time (τ(complete)) required to achieve complete isoflavone glycosides deglycosylation, were 0.35 ± 0.04 min(-1), 2.04 ± 0.25 min, and 30 min (for daidzin) and 0.65 ± 0.03 min(-1), 1.19 ± 0.08 min, and 20 min (for genistin), respectively. HPLC results revealed that this enzyme system took only 30 min to reach complete isoflavone deglycosylation and the aglycone content in the total isoflavones in black soymilk was enriched by 51.42 ± 0.17% under a 30 min treatment by the glass microsphere enzymatic system.