Effective decontamination methods are essential for minimizing the presence of harmful microorganisms in fresh foods. The incorporation of bioactive compounds in packaging processes stands out as one of the most effective approaches to maintain food quality and enhance food safety. This study focuses on the synthesis of a conjugate, CS-ZnPPIX, formed by linking Zn(II) protoporphyrin IX with chitosan. The aim was to create a naturally derived polymeric material capable of reducing microbial contamination in food packaging through the photodynamic inactivation (PDI) of pathogens. The CS-ZnPPIX film displayed a homogeneous coating of the surfaces. Its absorption and emission spectra showed characteristic Zn(II) porphyrin bands, along with a fluorescence quantum yield of 0.054. Photodynamic analysis indicated that CS-ZnPPIX could generate singlet oxygen (Φ_Δ = 0.49) and superoxide anion radicals. In vitro experiments with the Gram-positive bacterium Staphylococcus aureus revealed that exposure to 1 μM CS-ZnPPIX followed by 30 min of white light irradiation led to effective bacterial eradication (> 7 log, 99.9999% reduction in survival). Additionally, this study evaluated the effectiveness of PDI in reducing S. aureus contamination on food packaging materials. CS-ZnPPIX proved effective in decontaminating surfaces made of polyethylene terephthalate, expanded polystyrene, glass, and aluminum packaging materials. Treatment of these bacteria-laden surfaces with 0.54 nmol CS-ZnPPIX and subsequent 30 minutes of irradiation resulted in more than a 5 log reduction (99.9998%) in bacterial survival. Furthermore, this procedure effectively eliminated individual pathogen cells attached to surfaces. The merit of this conjugate, compared to other methods of surface sterilization, primarily lies in its economic and sustainability benefits due to its low production cost. Furthermore, the natural origin of the polymer helps maintain a safe profile, minimizing environmental contamination. Consequently, the CS-ZnPPIX conjugate demonstrates promising properties for decontaminating packaging, achieving aseptic packaging materials, and aiding in food preservation.