Polysaccharide chitin (CH) was modified by antimicrobial natural gum rosin as a biocompatible agent within the thermoplastic polyurethane (TPU) elastomer to form the TPU/CH composite. This blend was then mixed with different ratios of ZnO-doped-SiO2 nanoparticles (ZnO-SiO2-NPs) to chelate chitin and to improve the properties of TPU nanocomposites. The topology and surface roughness of chitin and nanoparticles within the TPU matrix, besides their effect on the crystallinity degree of TPU were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), and X-ray diffraction (XRD). The TPU nanocomposites are subjected to different measurements such as mechanical, thermal, hydrophobicity, flammability, water vapor, and oxygen barrier properties, as well as antimicrobial activity. The results showed that the major properties were improved when the nanoparticles were added, especially at 5 wt%. Furthermore, the TPU/CH blend reinforced with high contents of NPs (i.e., 5–7 wt%) exhibited efficient antimicrobial activities against Gram-negative, Gram-positive bacteria and, pathogenic fungi.