Interactions between a widely used polycationic polymer, polyethyleneimine (PEI), and a Gram-negative bacteria, E. coli, are investigated using atomic force microscopy (AFM) quantitative imaging. The effect of PEI, a known membrane permeabilizer, is characterized by probing both the structure and elasticity of the bacterial cell envelope. At low concentrations, PEI induced nanoscale membrane perturbations all over the bacterial surface. Despite these structural changes, no change in cellular mechanics (Young’s modulus) was detected and the growth of E. coli is barely affected. However, at high PEI concentrations, dramatic changes in both structure and cell mechanics are observed. When immobilized on a flat surface, the ability of PEI to alter the membrane structure and reduce bacterial elasticity is diminished. We further probe this immobilization-induced effect by covalently attaching the polymer to the surface of polydopamine nanoparticles (PDNP). The nanoparticle-immobilized PEI (PDNP-PEI), though not able to induce major structural changes on the outer membrane of E. coli (in contrast to the flat surface), was able to bind to and reduce the Young’s modulus of the bacteria. Taken together, our data demonstrate that the state of polycationic polymers, whether bound or free—which greatly dictates their overall configuration—plays a major role on how they interact with and disrupt bacterial membranes.