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Precision intracellular sensing, probing and manipulation offer unprecedented opportunities for advances in biological sciences. Next-generation ultra-fine probes will be capable of targeting individual cell organelles. Development of such probes as well as probes capable of penetrating through tough cell walls requires detailed knowledge of cell-probe interaction. This Letter evaluated the applicability of environmental scanning electron microscopy (ESEM) for cell and cell-probe interaction imaging. Several types of cells (plant and yeast cells as well as mouse spermatozoa) were successfully imaged in their natural state, with mouse spermatoza observed by ESEM for the first time. Computerised stage applied to image was tough plant cell walls interactions with several probes. Substantial damage to the cell walls was observed as a result of microprobe penetration. The damage persisted after the probe withdrawal and there was residue of cellular content on the withdrawn probes. Several mechanisms of probe failure were observed in situ global buckling, localised bending followed by the tip break-off, and plastic deformation with permanent bending in the case of ultra-fine metal nanoprobe. The results demonstrate applicability of ESEM for high-resolution in situ imaging of cells. Observed mechanisms of cell damage and probe failure provide guidance for future development of probes for minimally-invasive intercellular probing.