Ion bombardment of living cellular material is a novel subfield of ion beam surface modification that is receiving growing attention from the ion beam and biological communities. Although it has been demonstrated that the technique is sound, in that an adequate fraction of the living cells can survive both the vacuum environment and energetic ion bombardment, there remains much uncertainty about the process details. Here we report on our observations of onion skin cells that were subjected to ion implantation, and propose some possible physical models that tend to support the experimental results. The ion beams used were metallic (Mg, Ti, Fe, Ni, Cu), mean ion energy was typically 30keV, and the implantation fluence was in the range 1014–1016ions/cm2. The cells were viewed using Atomic Force Microscopy, revealing the formation of microcrater-like structures due to ion bombardment. The implantation depth profile was measured with Rutherford backscattering spectrometry and compared to the results of the TRIM, T-DYN and PROFILE computer codes.