The consumption of fruits and vegetables in the daily diet is an adequate condition for obtaining a healthy life. Therefore, decontamination is crucial to reducing the appearance of potentially dangerous microorganisms in these foods. In this work, a conjugate (CS−PPIX) of natural origin was synthesized from the covalent union of protoporphyrin IX (PPIX) and chitosan (CS) by amide bonds. This photosensitizer was developed to reduce the microbial load in fruits and food packaging through the photodynamic inactivation of microorganisms (PDI). A film of CS−PPIX showed an appreciable contact surface. The conjugation of PPIX to CS was confirmed by IR spectra. The absorption and emission spectra of the conjugate exhibited the characteristic PPIX bands, accompanied by a fluorescence quantum yield of 0.10. Photodynamic investigation indicated that CS−PPIX produced singlet molecular oxygen (Φ Δ = 0.40) in solution. Also, this compound was able to generate superoxide anion radicals with the assistance of the reductant nicotinamide adenine dinucleotide and efficiently photo-oxidize the amino acid L-tryptophan. PDI in vitro experiments were performed with the Gram-positive bacterium Staphylococcus aureus. Bacteria were eliminated (>99.9999% reduction in survival) when cell suspensions were treated with 1 μM CS−PPIX upon 30 min of irradiation with white light. Furthermore, no microbial growth was detected in cells immobilized on agar surfaces in the CS−PPIX-treated areas. Therefore, the PDI approach was evaluated to reduce the contamination of S. aureus on fruit surfaces and food containers. After treating the surfaces of apple and pear pieces with 10 nmol of CS−PPIX, a greater than 99.9% reduction in bacterial survival was observed upon an irradiation of 30 min. This conjugate was also effective in the photodynamic decontamination of polyethylene bags and polyethylene terephthalate packaging materials. Therefore, the CS−PPIX conjugate presents adequate properties to reduce the microbial load and preserve fresh foods.