The unique properties of graphene make it an ideal material for electrochemical studies, particularly of the electrochemical double-layer. However, experimental studies generally require depositing graphene on substrates like gold, that may affect the electronic structure of the electrode and thus the ions adsorption properties. This study explores the impact of gold substrates on graphene electrochemical behavior using molecular dynamics. Two systems were compared: graphene on gold (Gr@Au) and standalone graphene (Gr), with ionic liquid ([EMIM][TFSI]) as the electrolyte. The model accounts for the different metallic behavior of graphene and gold under the various applied potentials. Despite a similar electrolyte structure, the interfacial capacitance is affected, which can be attributed to different charge distributions within the electrode. The variations of the van der Waals and Coulomb energies also show some differences in the presence of gold, in particular for low potentials.