The isolated Aspergillus ochraceus was utilized to create silver and selenium nanoparticles (AgNPs and SeNPs) using its cell-free filtrate. Particle sizes for SeNPs ranged from 32.3 to 50.7 nm, whereas those for AgNPs ranged from 6.41 to 11 nm. The biosynthesized NPs were mixed with either sodium alginate or chitosan formation of food packaging film. Using scanning electron microscopy, ultraviolet-visible spectroscopy (UV-Vis), and Fourier transform infrared spectroscopy, the produced films were functionally and morphologically characterized. Composite films were tested for biodegradability, cytotoxicity, water vapor transmission rate, mechanical strength, solubility, and antifungal activity. When comparing SA/NPs with CS/NPs, the latter had superior biological, mechanical, antifungal and antioxidant properties. In the case of nanocomposite films containing CS/AgNPs, CS/SeNPs, SA/AgNPs, and SA/SeNPs, respectively, the tensile strength of CS (0.58 MPa) or SA (2.42 MPa) increased to 4.15 MPa, 4.16 MPa, 3.07 MPa and 2.48 MPa. However, for CS/AgNPs, CS/SeNPs, SA/AgNPs, and SA/SeNPs, respectively, the water vapor pressures decreased from 2021.57 g/m2.day for CS and 2132.59 g/m2.day for SA to 1559.94, 1518.93, 1945.24 and 1775.96 g/m2.day. For CS/AgNPs, CS/SeNPs, SA/AgNPs, SA/SeNPs, CS, and SA, the corresponding statistical minimum inhibitory concentrations were 1020, 1040, 1080, 1025, 1160, and 1160 µg/ 5 mL. When formed films compared to films made of plastic, the nanocomposite films with NPs significantly reduce Penicillium citrinum contamination. Specifically, the produced CS/SeNPs films show a lot of promise as non-toxic antimicrobial active packaging components that could prolong the freshness of fruits and other foods.