The cellular response of MCF-7 cells after uptake of pristine carbon nanodots (CNDs) was investigated by MS-based proteomics and secretomics. Only minor changes in the proteomes and secretomes were observed independetly from the medium (full medium: RPMI1640 with FBS/PS/L-Glu, basal medium: RPMI1640 without additives, or starvation medium: Earle's Balanced Salt Solution (EBSS)). Further investigations showed that even under high CND concentrations, the lysosomal functionality, as characterized via cathepsins B and L as well as the autophagic markers SQSTM1/p62 and LC3B, is maintained. Furthermore, branched polyethylenimine (bPEI) molecules have been coupled to the CNDs as a model functionalization or example of a drug. We observed that the bPEI-CND conjugates accumulate to a higher degree in the lysosomes as compared to bPEI or CND alone. Here, changes in the lysosomal size and function were observed, which can be explained exclusively by the bPEI. It is concluded that CNDs are highly efficient and inert carriers for functional molecules into lysosomes as target, with the added value that lysosomal escape is suppressed, thereby avoiding unintended side effects in other cellular compartments.