The fabrication of hybrid protein-Cu3(PO4)2 nanoflowers (NFs) via an intermediate toroidal structure is dramatically accelerated under shear using a vortex fluidic device (VFD), which possesses a rapidly rotating angled tube. As-prepared laccase NFs (LNFs) exhibit ≈1.8-fold increase in catalytic activity compared to free laccase under diffusion control, which is further enhanced by ≈ 2.9-fold for the catalysis under shear in the VFD. A new LNF immobilization platform, LNF@silica incorporated in a VFD tube, was subsequently developed by mixing the LNFs for 15 min with silica hydrogel resulting in gelation along the VFD tube surface. The resulting LNFs@silica coating is highly stable and reusable, which allows a dramatic 16-fold enhancement in catalytic rates relative to LNF@silica inside glass vials. Ultraviolet-visible spectroscopy-based real-time monitoring within the LNFs@silica-coated tube reveals good stability of the coating in continuous flow processing. The results demonstrate the utility of the VFD microfluidic platform, further highlighting its ability to control chemical and enzymatic processes.