Over the last decade, the interest in carbon dots, graphene dots, or similar carbon-based nanoparticles has increased considerably. This interest is based on potentially high fluorescent quantum yields, controllable excitation-dependent emission, low toxicity, and convenient reaction conditions. Carbon dots are often seen as a promising alternative to classical semiconductor quantum dots that are typically made from toxic semiconductor materials. Surprisingly, aspects like the atomic structure, composition, mechanism of formation, and precise understanding of the photophysical properties of carbon dots are still mostly unknown. The large number of different precursor systems and the variety in synthesis routes make a direct comparison of different systems difficult. To advance this, we went for a systematic approach and compared the results of four synthesis routes using two different precursor systems. We used different spectroscopy and microscopy methods including fluorescence correlation spectroscopy to characterize the different reaction products. We found that for syntheses solely based on citric acid as the precursor, we obtain particles where the emission wavelength is strongly dependent on the excitation wavelength despite relatively low quantum yields. In comparison, when urea is added as a nitrogen doping reactant, we observe vastly increased quantum yields. By making use of a combination of dialysis and column chromatography, we were able to isolate various luminescent species with high quantum yields and verify the existence of different molecular fluorophores. A detailed and consistent characterization of the reaction products during the course of purification revealed strong interactions between molecular fluorophores and larger reaction products.