Long-term cell tracking is a research interest for biological scientists across disciplines and applications. However, the long-term cell tracking experiments are often limited due to photobleaching and photo-toxicity. In the current study, a carbonaceous nanoprobe was developed by single step microwave assisted degradation of whey protein in aqueous phase. The CNDs were characterized via UV Vis spectroscopy, fluorescence spectroscopy, HRTEM, DLS and FTIR. Due to choice of the precursor, the CNDs were observed to be doped with sulfur and nitrogen. The CNDs were capable of bioimaging. In a 2D cell culture system (culture flask), up to five passages, the cells retained fluorescence. In a 3D microenvironment, also cell tracking was successful up to 10 days. The CNDs were observed to be capable of scavenging super oxides and hydroxyl radicals in vitro. CNDs were also observed to save cells from phototoxicity and UV exposure via cytotoxicity, microscopy and nanoindentation analysis.