Resumen: Disinfection treatments are necessary for the safe use of water, but Free-Living Amoebae (FLA) are known to resist conventional processes, posing a health threat to water users that increases due to the endosymbiont bacteria (EB) FLA can carry inside. Advanced Oxidation Processes are promising disinfection treatments that have been extensively studied on bacteria but have barely been studied on FLA or EB yet. For the first time, the inactivation efficiency of combining H2O2 and simulated solar radiation (SR) against Acanthamoeba and their EB was evaluated. Its performance was compared to only H2O2 and solar radiation (SR) at 280–800 nm. The influence of Acanthamoeba origin was also evaluated. Concentrations of 7 to 10 mM H2O2 were necessary for inactivating Acanthamoebae, but 25 mM was required to kill EB. SR was inefficient for the used-to-solar-exposure Acanthamoeba strain. H2O2/SR improved the disinfection efficiency of treatments alone. 5 mM of H2O2/SR for 5 min eradicated both Acanthamoebae and EB, reducing up to 6 and 30 times the H2O2 dose and the SR fluence necessary, respectively. The Acanthamoeba strain that had already overcome water treatments was more resistant to all the treatments than the freshwater strain. This study underlines the protective role of amoebae in disinfection processes and the wide pathogenic microorganism spectrum that can overcome water treatments thanks to this “trojan horse”. More research is needed to optimize conditions and establish H2O2/SR as an efficient disinfection treatment that prevents waterborne and nosocomial infections of endosymbiont microorganisms according to water use.