Dual nanoparticles endowed with emission photoswitching ability are produced by the flash coprecipitation of fluorophores and photochromes in water in order to investigate the mutual interplay between the self-assembled photoactive units as a function of their respective ratio. Photophysical studies show that high fluorophore/photochrome ratios favor very fast on/off fluorescence photoswitching, while the opposite is true for recovering emission thanks to the strong antenna effects permitted by the spatially confined entities in nanoparticles. Attempts to regenerate the initial state upon visible irradiation reveal unexpected structural transformations, which result from the noncovalent dye self-assemblies. Morphological investigations support phototriggered photochrome clustering within and around the fluorescent core of the dual nanoparticles after a UV-vis cycle or irradiation, causing partitioning of the photoactive units. The photoinduced morphological changes provide attractive prospects in the fabrication of smart drug delivery systems where active material release by external stimuli represents a very dynamic research area.