Abstract The uptake of fluorescently labeled ultrasmall gold nanoparticles (2 nm) by Gram‐negative Escherichia coli bacteria occurs within 1–3 hours. This was demonstrated by confocal laser scanning microscopy (CLSM), structured illumination microscopy (SIM), stochastic optical reconstruction microscopy (STORM), and flow cytometry. For imaging, eGFP‐expressing and DsRed2‐expressing E. coli strains were used in addition to non‐fluorescing E. coli strains. Gold nanoparticles were labeled with fluoresceine (FITC), Cy3, and AF647, respectively. Importantly, gold nanoparticles showed no toxicity to the bacteria, indicating a non‐lethal nature of the uptake, that is, not related to cell injury.