Novel organic‐inorganic polyoxometalates (POMs) decorated with covalent fluorescent tags have been designed for cell internalization. Their localization within model HEK cells is readily accomplished by confocal fluorescence microscopy. While cell internalization is dictated by the formation of the amphiphilic POM‐based nanostructures, their cytoplasmic‐nuclear trafficking appears to be regulated by a subtle interplay of the organic‐inorganic domains of the nanoassemblies which, in turn, impacts their dynamic behavior and capability to interact with cell membranes.