With an increasing emphasis on environmental protection and sustainability, natural polymers like proteins and polysaccharides are being utilized more frequently in the development of biodegradable food packaging. However, the limited properties of these biopolymers have restricted their widespread applicability within the food industry. To address this issue, eugenol-loaded zein nanoparticles (ZE NPs) were incorporated into pea starch/soy protein-based films, and their effect on the physicochemical properties of these films were investigated. The ZE NPs exhibited high compatibility with the pea starch-soy protein isolate (PES/SPI) matrix, enhancing the structural properties of the films by forming hydrogen bonds between the nanoparticles and the biopolymer network. Incorporating the nanoparticles enhanced the mechanical properties, thermal stability, ultraviolet shielding, surface hydrophobicity, and moisture barrier performance of the films. Furthermore, the films containing ZE NPs exhibited significant antioxidant and antibacterial activity, suggesting their potential application as preservatives in active food packaging materials. In conclusion, the incorporation of ZE NPs significantly enhanced the performance of PES/SPI-based films, which should expand their application as food packaging materials.