Ensuring microbiological safety is a growing concern in modern food technology, especially in response to consumer demand for minimally processed fruits and vegetables. In this study, two novel photosensitizer conjugates were synthesized by covalently linking protoporphyrin IX (PPIX) and its Zn (II) complex (ZnPPIX) to polyethyleneimine (PEI). The aim was to develop naturally derived polymeric materials capable of reducing microbial contamination on food surfaces through photodynamic inactivation (PDI) of pathogens. The conjugates were characterized by means of FT-IR spectroscopy, confirming successful covalent binding. Spectroscopic analysis indicated that the porphyrin chromophores retained their optical properties upon conjugation with PEI. Both PEI–PPIX and PEI–ZnPPIX were able to generate singlet oxygen (Φ_Δ = 0.20 and 0.47, respectively) and superoxide anion radicals in the presence of NADH. In addition, the conjugates efficiently photooxidized the amino acid L-tryptophan, a commonly used substrate in biological photochemistry. PDI assays demonstrated strong antimicrobial activity against Staphylococcus aureus, with both conjugates achieving >7 log reductions in bacterial viability. Furthermore, cucumber surfaces were used as a representative raw food commonly found in salads. After microbial contamination, both photosensitizers showed effective pathogen eradication at low concentrations (0.1–2.5 nmol). These results indicate that PEI–PPIX and PEI–ZnPPIX are promising antimicrobial materials with potential applications in the preservation of fresh food and extending shelf life.