A detailed stratigraphic investigation of the intercalation mechanism when graphite electrodes are immersed inside diluted perchloric (HClO₄) and sulfuric (H₂SO₄) electrolytes is obtained by comparing results when graphite crystals are simply immersed in the same acid solutions. By combining time-of-flight secondary ion mass spectrometry (ToF-SIMS) and in-situ atomic force microscopy (AFM), we provide a picture of the chemical species involved in the intercalation reaction. The depth intensity profile of the ion signals along the electrode crystal clearly shows a more complex mechanism for the intercalation process, where the local morphology of the basal plane plays a crucial role. Solvated anions are mostly located within the first tens of nanometers of graphite, but electrolytes also diffuse inside the buried layers for hundreds of nanometers, the latter process is also aided by the presence of mesoscopic crystal defects. Residual material from the electrolyte solution was found localized in well-defined circular spots, which represent preferential interaction areas. Interestingly, blister-like micro-structures similar to those observed on the highly oriented pyrolytic graphite (HOPG) surface were found in the buried layers, confirming the equivalence of the chemical condition on the graphite surface and in the underneath layers.