Antimicrobial peptides have been demonstrated to display an immediate response to a large set of pathogenic activity against viruses, bacteria, and fungi by virtue of their local binding with phospholipid phosphatidylserines to exert cytotoxic effect. Plasmonic nanostructures are particularly appealing in medical diagnostics and therapeutics owing to their biocompatibility and ease of surface modification. The current article reports a development of ε‐poly‐l‐lysine modified gold nanorod (PLL‐AuNR) Raman‐active system that can be used to target pathogenic bacteria along with rapid monitoring of antimicrobial action from environmental samples. Result indicates a remarkable change in Raman enhancement factor from 1.49 × 104 to 2.17 × 107 after addition of Salmonella, Bacillus subtilis, and Escherichia coli bacteria in PLL‐AuNR colloid, enabling a large optical window to monitor the process of pathogenic action. Antimicrobial assay with PLL‐AuNR reveals significantly high cytotoxic values of ~92% in E. coli, ~90% in B. subtilis, and ~87% in Salmonella compared with their respective responses in bare PLL, which shows ~37% in E. coli, ~32% in B. subtilis, and ~27% in Salmonella, which proportionally collaborates with change in surface‐enhanced Raman spectroscopy (SERS) intensity beyond 10 min of incubation time. Major experimental design parameters and possible mechanism that relates unusual plasmonic enhancement and antimicrobial action of PLL‐AuNR system have also been discussed.