Over the last years, the photo-Fenton process has been established as an effective, green alternative to chemical disinfection of waters and wastewaters. Microorganisms' inactivation is the latest success story in the application of this process at near-neutral pH, albeit without clearly elucidated inactivation mechanisms. In this review, the main pathways of the combined photo-Fenton process against the most frequent pathogen models (Escherichia coli for bacteria and MS2 bacteriophage for viruses) are analyzed. Firstly, the action of solar light is described and the specific inactivation mechanisms in bacteria (internal photo-Fenton) and viruses (genome damage) are presented. The contribution of the external pathways due to the potential presence of organic matter in generating reactive oxygen species (ROS) and their effects on microorganism inactivation are discussed. Afterwards, the effects of the gradual addition of Fe and H2O2 are assessed and the differences among bacterial and viral inactivation are highlighted. As a final step, the simultaneous addition of both reagents induces the photo-Fenton in the bulk, focusing on the differences induced by the homogeneous or heterogeneous fraction of the process and the variation among the two respective targets. This work exploits the accumulated evidence on the mechanisms of bacterial inactivation and the scarce ones towards viral targets, aiming to bridge this knowledge gap and make possible the further application of the photo-Fenton process in the field of water/wastewater treatment.