The process of formation of cobalt silicides near the graphene-silicon carbide interface by intercalation of single-layer graphene grown on the 4H- and 6H-SiC(0001) polytypes with cobalt and silicon is studied. The experiments were carried out in situ in ultrahigh vacuum. The analysis of the samples is performed by high-energy-resolution photoelectron spectroscopy using synchrotron radiation, low-energy electron diffraction, and also Raman spectroscopy, atomic-force and kelvin-probe microscopies. The thicknesses of the deposited cobalt and silicon layers is varied to 2 nm, and the sample temperature, from room temperature to 1000°C. Co and Si atoms deposited on heated samples is found to penetrate under graphene and are localized between the buffer layer and the substrate, which leads to a transformation of the buffer layer into additional graphene layer. It is shown that the result of intercalation of the system with cobalt and silicon is the formation under two-layer graphene of a Co–Si solid solution and silicide CoSi coated by the surface Co3Si phase. It is shown that the thickness and the composition of the formed silicide films can be changed by varying the amount of the intercalated material and the order of their depositions.