Shungite rocks of Karelia (Russia) form a large, diverse group of black sedimentary-volcanic Proterozoic (2.0 Ga) rocks with giant elemental carbon reserves (>25 × 1010 tonnes). The complex metamorphic history of these rocks and the unusual stuctural characteristics of shungite carbon have made it the subject of attention and controversy. The structure and microstructure of shungite carbon, subjected to contact metamorphism by intrusive dolerite sills overprinted by greenschist-facies regional metamorphism, were studied by Raman spectroscopy (RS), transmission electron microscopy (TEM), and selected-area electron diffraction (SAED). The RS, TEM and SAED data have revealed the characteristic structural features of shungite acquired during contact metamorphism and eventually preserved despite the subsequent metamorphic event. The microstructure of shungite affected by the most intense metamorphic transformation of all the analysed samples is characterized by hollow nanospheres with diameters of approximately 100 nm and a wall thickness of up to 10 nm (~ 30 graphene layers). The maximum degree of structural order in this shungite was recorded by RS study (R2 ca. 0.47) at the contact with the intrusive dolerite sills.