ZnAl2O4 and CuAl2O4 spinel nanoparticles were prepared by a modified Pechini method and used with the natural chitosan (CS) and shellac (SH) polymers to form novel composite membranes as promising food packaging materials. The selection of ZnAl2O4 and CuAl2O4 spinel nanoparticles was based on their antibacterial characteristics, availability, and economy. Using a straightforward and adaptable solution mixing and casting method, the bio-composites were created. The mechanical, physical, antibacterial, homogeneity and air permeability properties of composite films were investigated. The film structure was evaluated in terms of component interactions using FTIR spectra. The addition of 10% SH increased the tensile strength, percentage strain at maximum load, Young’s modulus, and burst strength by 114–101%, 3.6–8.4, 103–119, and 179–153% for low and middle M.wt./CS respectively. Chitosan/shellac-CuAl2O4 composite has superior properties compared to ZnAl2O4 composite. In general, 0.05% spinel provides a composite having better qualities than that of 0.1 additions. Middle M.wt. chitosan provides a composite with superior properties compared to that of low M.wt. The incorporation of ZnAl2O4 or CuAl2O4 enhanced the thermal stability of the SH/CS composite. ZnAl2O4 provides superior thermal stability than CuAl2O4. When shellac/CS film structure is treated with the previously indicated ZnAl2O4 or CuAl2O4 formulation, the % swelling decreases along with an increasing in the gel fraction. The antimicrobial assessment using inhibition zone diameter and shake flask methods showed that a composite of 1:9 shellac/chitosan/0.05% of CuAl2O4 exerted the highest Gram-positive antibacterial activity against B. mycoides (21 mm), and C. albicans (22 mm). So, these enhancements make chitosan/shellac/ZnAl2O4 or CuAl2O4 composite films a good alternative to producing food packaging materials.