In this work, we show that dopants (silver, copper and iron) significantly increase the antibacterial activity of ZnO nanoparticles. The shapes of ZnO and Ag-ZnO were spherical but it changed to nanoneedles and nanorod-nanosphere composite after doping with Cu and Fe, respectively. The nanoparticles exhibited increased reactive oxygen species (ROS) and metal ion release after doping. Electron microscopy images revealed that small size and sharp features of nanoparticles enable them to internalize and damage the cells, impairing the cell membrane integrity, causing cytoplasm leakage and cell shrinkage. Nanoparticles close to the cell wall indicate that physical attrition of nanoparticles with cells also plays a role in cell damage. The alterations in molecular biochemical composition of bacteria were probed by FTIR and it was seen that the nanoparticles not only affected phosphate and sugar vibrations of cell wall, but also distorted the alpha-helix and beta-sheets of the cellular proteins.