In this study, composite packaging films were produced from relatively inexpensive materials including whey protein isolate (WPI) and Persian gum (PG), supplemented with betanin nanoliposomes (NLPs). Using response surface methodology (central composite design), we investigated the effects of two variables (PG [0–2% w/v] and betanin NLPs’ [0–10% w/v] content) on the physico-mechanical and antioxidant properties of the film treatments. Afterward, the optimal treatment was evaluated for structural and antimicrobial characteristics. The film samples' permeability to water vapor decreased with the addition of NLP (from 7.38 to 5.46 g/Pa.s.m) but increased with PG incorporation; decreased solubility was observed when either substance was added. Mechanical properties like Young’s modulus and tensile strength were weakened by PG addition, but the incorporation of NLPs led to pronounced tensile strength. XRD analysis revealed improved crystallinity through NLPs’ addition. The presence of NLPs in the nanocomposite film resulted in an elevated level of antibacterial activity against Staphylococcus aureus, while the addition of both PG and betanin NLPs led to improved antioxidative activity (63.45%). Considering the results, PG/WPI films loaded with betanin NLPs could be introduced in active packaging applications for the shelf life extension of perishable food products.