We present functional studies of lysosomes in human cells after uptake of carbon nanodots (CNDs). 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-II, is maintained. Furthermore, branched polyethylenimine (bPEI) molecules have been coupled to the CNDs as a model functionalization or example of a drug. We observe 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 are 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.