Novel strategies, including phenotypic screenings directly in a host-pathogen system, are needed to discover new drugs against tuberculosis. We used amoebae such as Dictyostelium discoideum and Acanthamoeba castellanii as a host model for in vivo drug screenings. We developed assays to monitor the impact of chemicals and intracellular factors on bacteria health, growth, and virulence mechanisms and intrinsic host defenses. We used GFP fluorescent reporters for quantification of bacteria numbers. We validated the system using known first and second line antimycobacterial drugs.