The coupling of graphene with a ferromagnetic material opens opportunities for technological innovations in spintronics. To obtain this coupling it is necessary to control the elaboration of interfaces at the atomic scale. Here, we present results on cobalt intercalation between graphene and a buffer layer supported on a SiC(0001) substrate. As a result, we obtain cobalt islands covered by graphene whose local electronic properties are measured by scanning tunneling microscopy and spectroscopy. These islands reveal two very distinct shapes and properties. Small-islands with atomic height and very narrow size distribution and, more interestingly, flat cobalt nanodots lower than one nanometer high, that are encapsulated by graphene. Compared to a graphene monolayer on SiC, those nanodots exhibit very different spectroscopic signatures. Using dI/dV local differential conductance spectra together with an analysis of image potential surface states measured thanks to dz/dV spectra, we show that graphene on the nanodots is neutrally charged. Moreover, its 4.65 eV work function is surprisingly larger than the predicted value of 3.8 eV for graphene on Co. First principle calculations show that those Co nanodots can be seen as cobalt bilayer sandwiched between two carbon planes.