Cationic antimicrobial peptides (CAPs) are essential components of the innate immune system. Most CAPs exert antimicrobial effects via membrane-active mechanisms, while high concentrations of CAPs are associated with non-selective cytotoxicity. We originally hypothesized that a sub-lethal concentration of CAPs was able to exert antibacterial activity, by interacting with negatively charged nucleic acids, and not by damaging bacterial membranes. We selected pleurocidin (Ple) and Escherichia coli as experimental models of CAPs and bacteria, respectively. Whereas Ple distinctly acted on bacterial membranes in a concentration-dependent manner, the cell viability was almost similar regardless the peptide concentration. To address how Ple retained its antibacterial activity in a low concentration, we particularly focused on the induction of intracellular apoptosis-like death (ALD). Finally, it was suggested that a sub-lethal concentration of Ple led to ALD in E. coli, mediated by caspase-like protein and RecA. To the best of our knowledge, this is the first study showing that alterations of CAP mechanisms are concentration dependent in bacteria.