The Gram-negative bacterium Pseudomonas aeruginosa can be an opportunistic human pathogen that is naturally resistant to many antibiotics and often develops further multidrug resistance. The protein antibiotic group of L-type pyocins can clear lethal MDR P. aeruginosa infections in mouse lungs but their mode of action is unknown. In this study, we show with cryo-EM that L-type pyocins inhibit the P. aeruginosa BAM complex in a multi-step mechanism. In the pre-inhibition state, L-type pyocins bind to the extracellular loop 6 of BamA and in the full inhibition state, the C-terminal extension blocks the lateral gate from accepting nascent outer membrane proteins. With cryo-ET, we show that BAM inhibition is cytotoxic by the excessive formation of vesicles leading to outer membrane disruption. To determine the cellular consequences of L-type pyocin intoxication, we combine transposon-directed insertion site sequencing (TRADIS), transcriptomics, proteomics, finding that L-type pyocins inhibit the BAM complex, resulting from a loss of integrity of the outer membrane and ultimately cell death.