Antimicrobial photodynamic treatment (aPDT) is a light-based method developed for the inactivation of microorganisms. With the emergence of antifungal- and antibiotic-resistant microorganisms, aPDT has been suggested as a promising microbial control strategy. The treatment is based on a combination of visible light, a photosensitizer (PS), and molecular oxygen. Illuminating the PS with adequate light in the presence of oxygen will result in the generation of abundant reactive oxygen species (ROS), which further react with multiple targets within microbial cells and eventually cause cell death. The risk of resistance development is low due to the multi-target mode of action of aPDT. The efficiency of aPDT for microbial inactivation on foods can be affected by several factors such as type and characteristics of the PS, light source, food surface geometry, environmental aspects, and microbial characteristics. Although still a concept, the application of aPDT has gained rapid acceptance in many different agri-food products and associated processes, including food production, industrial processing, storage, distribution, and retail. Most of the in vitro aPDT studies have provided evidence of significant antimicrobial effects, including cases in which viability was reduced up to eight orders of magnitude. Strong antimicrobial performance of aPDT was also reported for studies involving variable food matrices, including fruit and vegetables, meat products, and milk. This review provides up-to-date information on advances in the application of aPDT in the agri-food sector, including suitable photosensitizers, sources of light, microbial inactivation efficiency, the role of food matrix composition, potentiation effects, inactivation mechanisms, and potential or prospective applications in the food industry and in other areas of agriculture. Even though the field of aPDT is advancing rapidly, future research should aim at some topics, including (1) the complete analysis of the effects of the treatment on food matrices, (2) the inactivation of currently-neglected food spoilage microorganisms, and (3) comprehensive field evaluation of aPDT for the control of plant diseases, all of which are necessary in order for the treatment to find widespread use in the agri-food sector. • aPDT is efficient at inactivating food spoilage microorganisms. • Chlorophyllin and curcumin are the natural PS of choice. • Fruit, vegetables, and meat are the most studied food matrices. • Future studies with thermophilic food spoilage organisms are needed. • Thorough food matrix analysis after treatment is still lacking.