We aimed to develop antimicrobial agents that satisfy biosafety considerations while exhibiting efficient antimicrobial activity. Peptide-capped silver nanoclusters (peptide@AgNCs) were designed. In addition, the antimicrobial activity and mechanism of peptide@AgNCs were studied. The hemolysis and cytotoxicity tests on mammalian cells were used to confirm the biocompatibility of peptide@ AgNCs. KLA@AgNCs exhibited dramatic antimicrobial activity without inducing significant cytotoxicity in mammalian cells. The KLA@AgNCs destroyed the integrity of the bacterial membrane and induced ROS accumulation, causing oxidative damage to biomolecules. The malfunction of the respiratory chain complexes I and V completely suppresses the energy production, ultimately accelerating the death of the bacteria. Our findings may advance the development of Ag-based nanomaterials with enhanced bactericidal activity and improved biocompatibility.