Observations of real-time changes in living cells have contributed much to the field of cellular biology. The ability to image whole, living cells with nanometre resolution on a timescale that is relevant to dynamic cellular processes has so far been elusive. Here, we investigate the kinetics of individual bacterial cell death using a novel high-speed atomic force microscope optimized for imaging live cells in real time. The increased time resolution (13 s per image) allows the characterization of the initial stages of the action of the antimicrobial peptide CM15 on individual Escherichia coli cells with nanometre resolution. Our results indicate that the killing process is a combination of a time-variable incubation phase (which takes seconds to minutes to complete) and a more rapid execution phase.