The synthesis of carbon quantum dots (CQDs) from high molecular weight biomass-derived precursors poses a significant challenge due to the complex molecular structures and low conversion efficiency. This work demonstrates a green, rapid, and sustainable continuous hydrothermal flow synthesis (CHFS) approach for nitrogen-doped carbon quantum dots (NCQDs) from various biomass-derived precursors, including high molecular weight polymeric sources like chitosan, lignin, and humic acid. We find that the precursor structure significantly impacts the size of the fabricated NCQDs and their optical properties. Citric acid, a low molecular weight precursor, yields NCQDs with excitation-independent emission, higher quantum yields, and low non-radiative losses, while NCQDs derived from polymeric precursors exhibit excitation-dependent, red-shifted, and lower efficiency emission. Theoretical calculations, performed to understand the configuration and distribution of nitrogen dopants within the NCQD structure, show that pyridinic and graphitic nitrogen atoms exhibit a strong preference to aggregate near the centre of the edge of the NCQD and not in the vertices nor in the graphitic core, thus affecting the HOMO and LUMO, bandgap, and light absorption and emission wavelengths. The life cycle assessment (LCA) analysis highlights the green and scalable advantages of the CHFS process for producing NCQDs compared to batch methods, making it a sustainable and economically viable approach for large-scale NCQD synthesis from high molecular weight biomass-derived precursors. Hence, the combination of experimental data and theoretical calculations provides a comprehensive understanding of the structure-property relationships in these NCQDs.