Multidrug resistant bacteria are a significant global health burden, and new treatment options are needed to ensure disease control. Bacteria have several resistance mechanisms including the ability to modify drug targets, and lifestyle adaptations including establishment of intracellular niches within host cells. Antibiotic treatments that target single molecules are most likely to lead to resistance development in bacteria, therefore, new classes of drugs with different mechanisms compared to single-target drugs are urgently needed. Antimicrobial peptides kill bacteria via a predominantly membrane-active mechanism, involving selective recognition and lysis of negatively charged lipids associated with bacterial cell membranes. Importantly, antimicrobial peptides with cell-penetrating properties (antimicrobial CPPs) can cross host cell membranes to access bacteria in the cytosol or sequestered in vesicles. By reaching bacteria that can establish intracellular niches, the likelihood of bacteria evading treatment and establishing drug resistance is further reduced. Here we report the broad-spectrum activity of two β-hairpin peptides from the horseshoe crab, tachyplesin I (TI) and polyphemusin I (PMI), toward pathogenic and non-pathogenic bacteria. Peptide analogues [I11A]TI and [I11S]TI maintain activity toward bacteria, but are less toxic to mammalian cells. This increased therapeutic window allows treatment of infected cells at higher concentrations, to significantly reduce survival of uropathogenic Escherichia coli (UPEC) inside host macrophages. Peptide-lipid binding studies suggest that TI and PMI peptides kill UPEC by selectively binding and disrupting bacterial cell membranes. Moreover, treatment of UPEC with sublethal peptide concentrations increases zinc toxicity and enhances innate macrophage antimicrobial pathways. These data validate antimicrobial CPPs as attractive leads for developing new drugs for treating UPEC infection and suggest that optimization of native peptide sequences can deliver effective leads for targeting bacteria in extracellular and intracellular environments.