Electronic devices based on graphene technology are catching on rapidly and the ability to engineer graphene properties at the nanoscale is becoming, more than ever, indispensable. Here, we present a procedure of graphene functionalization on SiC(0001) that paves the way towards the fabrication of complex graphene electronic chips. The procedure resides on the well-known ion-implantation technique. The efficiency of the working principle is demonstrated by the intercalation of the epitaxial graphene layer on SiC(0001) with Bi atoms, which was not possible following standard procedures. The investigation of the obtained graphene system reveals no clear spin-orbit coupling enhancement expected by theory in addition to the presence of residual structural defects. Our graphene/SiC(0001) intercalation procedure puts forward the ion-beam lithography to nanostructure and functionalize desired graphene chips.