Nanoparticles (NPs) can interact with biological systems, with either negative or positive consequences (potential risks or elimination of pathogenic bacteria). In this context, we investigate the morphology and physico-chemical properties of Escherichia coli bacteria interacting with silica NPs by Atomic Force Microscopy (AFM), this method providing access to topographic information and local rheological properties at the nm scale (with a discrimination between “hard”, NPs, and “soft”, bacteria, materials), either in air or physiological environment. AFM images show that silica NPs tend to aggregate around bacteria, their further action depending on their diameter. The presence of big NPs (100 and 200 nm) does not change E. coli morphology, bacteria remaining rod-shaped and high. The bacterial external membrane keeps also its organization in domains, suggesting that such NPs are too voluminous to penetrate into bacteria. On the contrary, in the presence of small NPs (4 and 10 nm) bacteria adopt unusual spherical shapes, some of them even suffering from a partial collapse, leading to the release of cellular compounds. The external membrane is also disturbed, exhibiting spherical aggregates, which could be due to a reorganization of lipopolysaccharides present in this membrane.