Herein we report an expeditious and facile sonochemical synthesis method that takes just a few minutes to produce organic‐inorganic hybrid nanoflowers and their application as a nanobiocatalyst. Surfactant treated Burkholderia cepacia lipase was used as the organic component and manganese sulfate as the inorganic component to synthesize the nanoflowers in less than 10 minutes. Careful investigation of the process parameters was performed to obtain the optimized value for each attribute viz. sonication time (7.5 min), lipase concentration (0.1 mg/mL), MnSO4 concentration (150 mM), sonication frequency (33 kHz) and pH (8.0). An additional post‐synthesis treatment of nanoflowers with N‐hydroxysuccinimide (NHS) increased their reusability to over nine cycles with an overall six‐fold increase in the activity. In addition, thermal stability was demonstrated through a twenty‐fold increase in the half‐life of immobilized lipase at 80 °C than in free form. The hybrid nanoflowers displayed a marked improvement in the kinetic resolution of racemic intermediates of metoprolol, a selective β‐1 blocker drug [C (%)=46.7, eep=96.5, E=156] and cloranolol, a non‐selective β‐blocker drug [C (%)=49.5, eep=96.0, E=157] compared to free lipase which signifies its importance as a nanobiocatalyst.