The study was carried out to understand the effect of silver–silica nanocomposite (Ag-SiO sub(2)NC) on the cell wall integrity, metabolism and genetic stability of Pseudomonas aeruginosa, a multiple drug-resistant bacterium. Bacterial sensitivity towards antibiotics and Ag-SiO sub(2)NC was studied using standard disc diffusion and death rate assay, respectively. The effect of Ag-SiO sub(2)NC on cell wall integrity was monitored using SDS assay and fatty acid profile analysis, while the effect on metabolism and genetic stability was assayed microscopically, using CTC viability staining and comet assay, respectively. Pseudomonas aeruginosa was found to be resistant to beta-lactamase, glycopeptidase, sulfonamide, quinolones, nitrofurantoin and macrolides classes of antibiotics. Complete mortality of the bacterium was achieved with 80 mu g ml sup(-1) concentration of Ag–SiO2NC. The cell wall integrity reduced with increasing time and reached a plateau of 70% in 110 min. Changes were also noticed in the proportion of fatty acids after the treatment. Inside the cytoplasm, a complete inhibition of electron transport system was achieved with 100 mu g ml sup(-1) Ag-SiO sub(2)NC, followed by DNA breakage. The study thus demonstrates that Ag-SiO sub(2)NC invades the cytoplasm of the multiple drugresistant P. aeruginosa by impinging upon the cell wall integrity and kills the cells by interfering with electron transport chain and the genetic stability.