This study develops a novel dual-layer chitosan (CS)/pectin film incorporating grape skin anthocyanin extract (GSAE) and lignin to address critical limitations in cherry preservation. Unlike traditional methods that leave harmful residues, this bilayer design separately integrates functional components: GSAE for targeted antioxidant/antibacterial action and lignin for ultraviolet (UV) blocking. This targeted incorporation enables synergistic performance unattainable with single-layer or conventional approaches. The films, fabricated with lignin concentrations from 1% to 15% (w/v), demonstrated excellent mechanical integrity (assessed with structural characterization), optimized gas barrier performance, and effective UV attenuation (achieved via lignin incorporation). Antibacterial analyses confirmed substantial inhibition against Staphylococcus aureus and Escherichia coli. Crucially, cherry preservation tests showed that the 15% lignin film (PG/CL15%) reduced weight loss, preserved firmness, and extended shelf life by 8 days—a significant quantitative improvement over uncoated fruit. Structural characterization (TGA, FT-IR, and XRD) verified successful GSAE/lignin embedding via hydrogen bonding. Beyond cherries, this dual-layer, bio-based design offers a promising template for the active packaging of other perishable produce sensitive to oxidation, microbial spoilage, and UV degradation, which enhances its industrial relevance.