This work systematically compares both structural features and photocatalytic performance of a series of graphitic and amorphous carbon dots (CDs) prepared in a bottom-up manner from fructose, glucose, and citric acid. We demonstrate that the carbon source and synthetic procedures diversely affect the structural and optical properties of the CDs, which in turn unpredictably influence their photo electron transfer ability. The latter was evaluated by studying the photo-reduction of methyl viologen. Overall, citric acid-CDs were found to provide the best photocatalytic performance followed by fructose- and glucose-CDs. However, while the graphitization of glucose- and citric acid-CDs favored the photo-reaction, a reverse structure–activity dependence was observed for fructose-CDs due to the formation of a large graphitic-like supramolecular assembly. This study highlights the complexity to design in advance photo-active bio-based carbon nanomaterials.