Bacterial cellulose (BC), known for its exceptional physical properties and sustainability, has garnered widespread attention as a promising alternative to petrochemical-based plastic packaging. However, application of BC for packaging remains limited due to its hygroscopic nature, poor food preservation capabilities, and low optical transparency. In this study, a novel in-situ spraying method for chitosan (CS) encapsulation was developed to fabricate BC/CS hybrid structure layer by layer. The resulting composites exhibit effective antimicrobial activity against both Gram-positive and Gram-negative (> 75 %) bacteria, ensuring food preservation and safety. The BC/CS composites were modified through mercerization and heat drying (mBC/CS), transforming the cellulose crystal structure from cellulose I to the more stable cellulose II and inducing the alignment of a compact structure. Following waterborne polyurethane (WPU) coating, the mBC/CS/WPU composites acquired hydrophobic and heat-sealable properties, along with an 80 % reduction in haze and light transmittance exceeding 85 %. Further, they exhibited exceptional mechanical properties, including an ultimate tensile strength exceeding 200 MPa and omnidirectional flexibility. These composites could also preserve the freshness of sliced apples (< 20 % weight loss) and poached chicken (< 3 % weight loss) after one week of storage, comparable to commercial zipper bags, and also prevent food contamination. Notably, the mBC/CS/WPU composites displayed no ecotoxicity during decomposition and degraded completely within 60 days in soil. This study provides a valuable framework for functionalizing BC-based materials, promoting sustainable packaging, and contributing to the mitigation of plastic pollution.