This work describes that bacterial cellulose was successively modified by copper/zinc nanoparticles with the help of direct current and radio frequency magnetron sputter-coating method for electromagnetic interference shielding to enhance its hydrophobic, mechanical, and conductive properties. The surface morphology and properties of bacterial cellulose/copper/zinc nanocomposite were analyzed by various testing methods (X-ray photoelectron spectroscopy, X-ray diffraction) and instruments to analyze smooth deposition of metallic nanoparticles. The conductive and shielding effects were examined by a four-point probe and vector analyzer. The mechanical properties were investigated by a uniaxial testing machine. The combined structure of bacterial cellulose, copper, and zinc nanoparticles (Zn–Np) improves the surface hydrophobicity, mechanical strength, as well as electromagnetic interference shielding effectiveness, while zinc nanoparticles act as a protective layer over the surface of bacterial cellulose/copper nanocomposite. So, the findings revealed that the bacterial cellulose/copper/zinc nanocomposite has excellent hydrophobic ( θ; 143.7°), good mechanical (T.F; 39.67 MPa, elongation; 13.1%, Y.M; 5.90 MPa), conductive (50 W; 0.0323 S/m), and electromagnetic interference shielding (28.54 dB) properties.