In the last decade, the interest toward the formulation of polymer films for cultural heritage protection continuously grew, and these films must be imperatively transparent, removable, and should not react/interact with surface of the artworks. In this research, bionanocomposite films, based on chitosan (Ch) and pectin (P) and containing naturally occurring fillers and antioxidants, were formulated by solvent casting methods and were accurately characterized. The natural halloysite nanotubes (HNT) have a two-fold role, specifically, physical compatibilizer and antioxidant carrier. Therefore, the theoretical solubility between Ch and P was estimated considering Hoy’s method for solubility of polymers, while the optimum ratio between biopolymer constituents was assessed by ζ-potential measurements. The transparency, wettability, and mechanical behavior of Ch:P films, also in presence of HNT without and with antioxidants, were investigated. The beneficial effects of natural antioxidants, such as vanillic acid (VA) and quercetin (Q), on Ch:P/HNT durability were found.