The controversial nature of the fluorescent properties of carbon dots (CDs), ascribed either to surface states or to small molecules adsorbed onto the carbon nanostructures, is an unresolved issue. To date, an accurate picture of CDs and an exhaustive structure-property correlation are still lacking. Using two unconventional spectroscopic techniques, fluorescence correlation spectroscopy (FCS) and time-resolved electron paramagnetic resonance (TREPR), we contribute to fill this gap. Although electron micrographs indicate the presence of carbon cores, FCS reveals that the emission properties of CDs are based neither on those cores nor on molecular species linked to them, but rather on free molecules. TREPR provides deeper insights into the structure of carbon cores, where C sp2 domains are embedded within C sp3 scaffolds. FCS and TREPR prove to be powerful techniques, characterizing CDs as inherently heterogeneous systems, providing insights into the nature of such systems and paving the way to standardization of these nanomaterials.