Changes in agricultural practices, individual diversity, the considerable size of the global food trade, immigrant and tourist circulation, with microorganism transformations have led to the formation of microorganisms that are resistant to chemicals and implementations used, especially antibiotics. Antimicrobial photodynamic therapy (aPDT) is an approach based on the interaction of a natural/synthetic photosensitizer, a suitable light source, and molecular oxygen, and the cytotoxic effect of reactive oxygen species resulting from this interaction on the target microorganism. The benefits of this method, which has found its place in medical terms by treating oral biofilms, superficial lesions, and chronic sinusitis, are limited by problems of low cell/tissue penetration, poor selectivity, non-thermal effect, and off-target damage. Despite similar practical problems in food science, developing technology is expected to encourage new studies on pathogen inactivation in food matrices, reducing the microbial load to safe levels, extending shelf life, and preventing quality loss.