Various molecular fluorophores have been identified to be present during carbon-dot (C-dot) syntheses. However, the organization of such fluorophores in C-dots is still unknown. We study the self-assembly of 5-oxo-1,2,3,5-tetrahydroimidazo-[1,2-α]-pyridine-7-carboxylic acid (IPCA), a molecular fluorophore present during the synthesis of C-dots from citric acid and ethylenediamine. Both forms of IPCA (neutral and anionic) show a tendency to self-assemble into stacked systems, forming seeds of C-dots during their synthesis. IPCA also interacts with graphitic C-dot building blocks, fragments easily, and incorporates into their structures via π-π stacking. Both IPCA forms are able to create adlayers internally stabilized by an extensive hydrogen bonding network, with an arrangement of layers similar to that in ordinary graphitic C-dots. The results show the tendency of molecular fluorophores to form organized stacked seeds of C-dots and incorporate into C-dot structures. Such noncovalent structures can be further covalently interlinked via the carbonization process during C-dot growth.