Peptides carrying different fluorophores can be designed to incorporate spontaneously into living cells when added to the medium. By incorporating the peroxisome-targeting sequence PTS1, the peptide is recognized by the protein-import machinery of peroxisomes and, as a result, can accumulate in these organelles. Depending on the cell type, an inhibitor of the multidrug-resistance protein might be required to ensure strong accumulation. In this update, we discuss the potential of these peptide-linked fluorophores in solving issues related to organelle function and dynamics.