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A range of novel BODIPY derivatives with a tripodal aromatic core was synthesized and characterized spectroscopically. These new fluorophores showed promising features as probes for in vitro assays in live cells and offer strategic routes for further functionalization towards hybrid nanomaterials. Incorporation of biotin tags facilitated proof‐of‐concept access to targeted bioconjugates as molecular probes. Computational explorations using DFT and TD‐DFT calculations identified the most stable tripodal linker conformations and predicted their absorption and emission behavior. The uptake and speciation of these molecules in living prostate cancer cells was imaged by single‐ and two‐photon excitation techniques coupled with two‐photon fluorescence lifetime imaging (2P FLIM). [ABSTRACT FROM AUTHOR]