This study aimed to enhance solar disinfection (SODIS) by the photo-Fenton process, operated at natural pH, through the re-utilization of fruit wastes. For this purpose, pure organic acids, present in fruits and alimentary wastes were tested and compared with synthetic complexing agents. Owing to solar light, complexes between iron and artificial or natural chelators can be regenerated through ligand-to-metal charge transfer (LMCT) during disinfection. The target complexes were photoactive under solar light, and the Fe:Ligand ratios for ex situ prepared complexes were assessed, achieving a balance between iron solubilization and competition with bacteria as a target for oxidizing species. In addition, waste extracts containing natural acidic ligands are active agents for disinfection. Indeed, lemon and orange juice or their peel infusions turned out to be more efficient than commercially available organic acids, leading to complete inactivation in less than 1 h in the presence of Fe(II) and H2O2. Finally, application in Lake Leman water and in situ complex generation led to effective bacterial inactivation, even in mildly alkaline surface waters. This work leads to interesting SODIS and photo-Fenton enhancements for bacterial inactivation in resource-poor contexts and/or under the prism of circular economy.