In this paper, the study of three types of graphite electrodes in two types of ionic liquid solutions (ILs) using in situ Raman spectroscopy and X-ray diffraction in conjunction with electrochemical techniques such as voltammetry is described. The graphite materials included two types of synthetic flakes, differing from each other in their average particle size, and natural graphite flakes. The ILs included 1-methyl-1-propylpiperidinium bis(trifluoromethyl sulfonyl)imide (MPPp-TFSI) and 1-methyl-1-butyl pyrrolidinium bis(trifluoromethyl sulfonyl)imide (BMP-TFSI). The Li salt was Li TFSI. The graphite electrodes can intercalate with both Li ions and IL cations simultaneously. The latter intercalate with graphite at higher potentials (the onset potential is >0.7 V). The graphite electrodes develop passivation in the above Li TFSI/Li solutions upon their cathodic polarization, which blocks the intercalation of the IL cations but allows highly reversible intercalation with lithium. In situ Raman spectroscopy proved to be a very useful tool for studying both Li and IL cation intercalation processes with graphite electrodes and for determining their onset and reversibility. The effectiveness of the passivation of graphite electrodes in these solutions depends on both the type of graphite used and the structure of the IL cations. The most effective passivation, developed during a first cathodic polarization of the electrodes, was found for natural graphite electrodes and for MPPp+-based solutions. The important factors that may determine the performance of graphite electrodes in these systems are discussed.