A new hybrid bionanomaterial composed of zinc oxide nanoparticles (ZnO NPs) and chitosan was constructed after enzymatic immobilization of papain for biomedical applications. In this work, we report the preparation and characterization steps of this bionanomaterial and its biocompatibility in vitro. The properties of the immobilized papain system were investigated by transmission electron microscopy, zeta potential, DLS, UV–vis absorption spectroscopy, FTIR spectroscopy, and X-ray diffraction. The prepared bionanomaterial exhibited a nanotriangular structure with a size of 150 nm and maintained the proteolytic activity of papain. In vitro analyses demonstrated that the immobilized papain system decreased the activation of phagocytic cells but did not induce toxicity. Based on the results obtained, we suggest that the novel bionanomaterial has great potential in biomedical applications in diseases such as psoriasis and wound