Peptide-based antimicrobial biomaterials hold considerable promise to treat the prevalent infections caused by multidrug-resistant (MDR) pathogens. However, their clinical translation is hampered by high toxicity, proteolytic degradation, and poorly understood in vivo efficacy. Here, we present a novel multi-functional blocks intelligent combination approach to create low-toxicity and proteolytic-resistant self-assembled peptide dendrimer aggregates (SPDAs) that exhibit low-micromolar activity (≤4 μM) against gram-negative bacteria and MDR Escherichia coli. We investigated the in vivo biosafety of SPDAs and found that they were substantially less systemically toxic than polymyxin B at the same dose. In a peritonitis-sepsis mouse model, the SPDAs demonstrated significant in vivo therapeutic potential for the treatment of MDR E. coli infections. Importantly, the antimicrobial activity of the SPDAs was exerted via multimodal mechanism that included rapid plasma membrane rupture, interference with cellular growth and metabolism, and triggering reactive oxygen species accumulation. Collectively, SPDAs show tremendous promise in addressing the prevalent infections caused by MDR gram-negative pathogens, and these findings may offer unique insights that will inspire the development of novel peptide-based therapeutics.