The functionalization of graphene is a well-established route for modulating its optoelectronic properties for a wide range of applications. Here, we studied, using photoemission spectroscopies and synchrotron radiation, the band structure upon evaporation of a p-type dopant tetrafluoro-tetracyanoquinodimethane (F4-TCNQ) molecules and determined the work function (WF) shift over a large area of epitaxial graphene grown on a 4H-SiC (0001) silicon carbide substrate. This system exhibits peculiar nanostructures composed of mono and multilayers, notably at the step edges where the electronic properties differ from the terraces. We observed, owing to the high spatial resolution of photoemission electron microscopy (PEEM), that after the adsorption of F4-TCNQ, multilayer graphene on step edges was subjected to less charge transfer compared to the monolayer graphene on terraces, making their final WF smaller. We calculated the thermoelectric properties of this functionalized graphene system by using density functional theory and Boltzmann transport formalism within the range of the Fermi level (EF), and the carrier concentration, which was experimentally determined. We show that the Seebeck coefficient (S) on the nanofacets is 25% larger than on the monolayer terraces, and the maximum power factor (PF) is on the order of 10−2 W/K2m. This order of magnitude is comparable to the PF of commercial thermoelectric materials such as bulk bismuth telluride.