Recently, molecular fluorophores were shown to be formed in the bottom-up chemical synthesis, contributing to the emission of carbon dots (CDs), derived from a citric acid precursor. We applied an ammonothermal synthesis toward CDs, employing two reactants citric acid and supercritical ammonia functioning as both solvent and precursor. The resulting nanoparticles are identified as amorphous aggregates of molecular fluorophores based on citrazinic acid derivatives, which resemble many of the emission features typically reported to be characteristic for CDs. The aggregates absorb and emit at short and long wavelengths of the spectrum, a feature prior ascribed to intrinsic CD core and surface states, respectively. We identify three emission states: a high energy and a low energy aggregate state as well as an energy transfer state between both. Energy transfer is triggered only upon excitation within a narrow high energy spectral range, resulting in a characteristic blue-green double emission. The high energy aggregate state exhibits a trapping mechanism elongating emission lifetime. To further analyze aggregated molecular fluorophores, we studied aqueous solutions and films of citrazinic acid and polyvinylpyrrolidone and demonstrated their concentration dependent optical behavior. Since fluorophore aggregates reproduce the emissive features of CDs, the contribution of sp²/sp³ carbonized products and graphitic domains to the emission features of CDs must be carefully evaluated in future studies.