The identification of noninvasive strategies to monitor dynamics within living organisms in real time is essential to elucidate the fundamental factors governing a diversity of biological processes. This study demonstrates that the supramolecular delivery of photoactivatable fluorophores in Drosophila melanogaster embryos allows the real-time tracking of translocating molecules. The designed photoactivatable fluorophores switch from an emissive reactant to an emissive product with spectrally-resolved fluorescence, under moderate blue-light irradiation conditions. These hydrophobic fluorescent probes can be encapsulated within supramolecular hosts and delivered to the cellular blastoderm of the embryos. Thus, the combination of supramolecular delivery and fluorescence photoactivation translates into a noninvasive method to monitor dynamics in vivo and can evolve into a general chemical tool to track motion in biological specimens.