Francisella tularensis is a gram-negative facultative intracellular bacterial pathogen that in humans and animals causes the fulminating zoonotic disease tularemia. Free-living amoeba, such as A. castellanii and D. discoideum, serve as environmental hosts of various intracellular pathogens. Epidemiology of F. tularensis is commonly associated with water-borne transmission in some parts of the world, including mosquitoes and amoebae as the host reservoir of bacteria in aquatic environment resources. In vitro studies demonstrated intracellular replication of F. tularensis within D. discoideum and A. castellanii cells. It has been established that crucial step in Francisella infection is entering the target cells by receptor mediated phagocytosis. This process has been shown to be meaningful in macrophages, arthropod-derived cells and amoeba cells. We used a water-borne amoeba A. castellanii and D. discoideum as surrogate macrophages as amoeba model systems to study influence of metabolic inhibitor methylamine on results of intracellular and extracellular life of F. novicida. For the first time we showed that methylamine has inhibitory effect on F. novicida entry and replication in D. discoideum and A. castellanii. The influence of different levels of infection was also examined and showed a dose-dependent effect on intracellular and extracellular infection. Moreover, methylamine was analyzed to observe whether in concentration of 100 mM induce cytopathogenicity in amoebae mentioned before. We conclude that F. novicida cannot entry and replicates in D. discoideum and A. castellanii after treated with 100 mM methylamine and that this concentration of inhibitor is not toxic to amoeba itself and can be used to inhibit receptor-mediated phagocytosis during Francisella infection.