Carbon-coated silicon has been synthesized by a thermal vapor deposition method using silicon powder and toluene/benzene vapors carried by a nitrogen carrier gas. It has been investigated under different charging/discharging modes. In all cases, the silicon lattice undergoes gradual destruction during lithium insertion/extraction. Lithium ion extraction from the silicon host matrix did not lead to the formation of an ordered silicon structure. In addition, no new ordered phases were detected. Impedance spectroscopy was applied to monitor the changes during the first lithium insertion/extraction. The results suggest that the material behaves differently than the typical single phase well-defined structures, from which is possible to extract the diffusion coefficient at all lithium insertion levels. Impedance spectra rather detected the phase transition and connected changes in the roughness of the phase boundaries between the Si/C and C/electrolyte. Estimation of the diffusion coefficient was possible only after deeper lithium insertion/extraction when the spectra pattern followed the predictions of the Randless model.