Biomolecule functionalisation of carbon nano-dots (CDs) greatly enhances their biocompatibility and applicability, however, little is known about their molecular structure. Using an arsenal of spectroscopic and analytical techniques, we provide new insights into the physical and electronic structure of uncoated and glycan-functionalised CDs. Our studies reveal that surface functionalisation does not always result in a homogenous corona surrounding the core, and the choice of carbohydrate significantly affects the electronic structure of the surface CD states. Further, the average surface coverage of an ensemble of CDs can be probed via transient absorption spectroscopy. These findings have implications for CDs targeted at interactions with biological systems or local sensors.