Phagocytosis and bacterial killing are major actors of innate immunity. Phagocytes use various mechanisms to destroy bacteria: acidification of phagosomes, production of reactive oxygen species, of antimicrobial proteins, or of degradative enzymes. We do not fully understand the relative importance nor the degree of specificity of each of these mechanisms against different species of bacteria. In this study, we use the unicellular soil amoeba Dictyostelium discoideum as a model organism to analyze intracellular killing of bacteria. We showed that the necessary mechanisms used to kill bacteria intracellularly differ between species of bacteria. We identified effectors for intracellular killing of K. pneumoniae (lysozyme AlyL, hydrolase Aoah, BpiC protein, and AplA porine), E. coli. (NoxA, and BpiC), and P. aeruginosa (BpiC). We then further characterized the mode of action of AlyL in the intracellular killing of K. pneumoniae.