The enzyme immobilization technique has been widely applied in biotechnology, biomedicine, and environmental remediation. In this research, carboxylated bamboo-based cellulose nanofibers (BCNFs) were obtained by one-step oxidation modification of bamboo fibers using ammonium persulphate. The surface carboxyl groups of the BCNFs were modified by a crosslinking agent and then combined with polyethylene imine (PEI) functionalized magnetic nanoparticles to construct a microreactor system for enzyme loading by the methods of electrostatic self-assembly and physical adsorption. Contrasted with free β-glucosidase, the microreactor possesses higher relative enzyme activity at pH 5.5 and 50℃, and the storage stability is significantly higher, with >75% relative enzyme activity after storage at 4℃ for 15 d. In addition, the β-glucosidase loaded on the microreactor facilitates its separation from the reaction medium and subsequent reuse. After completing five cycles of use, it retained 76.47% of its initial activity. The biotransformation of geniposide reached 93.10%, and the genipin concentration increased 1.2 folds higher than that in the original plant extract. Therefore, PEI@Fe₃O₄@BCNFs microreactor immobilized with β-glucosidase can be successfully used to produce higher activity aglucone such as genipin from geniposide, and it might also have the potential to convert phytochemicals by the immobilized enzyme microreactor system with bamboo-based cellulose nanofibers in the natural production field.