There is great interest in the self-organization of the proper subunits as a new strategy for the realization of fluorescent chemosensors. In this article, it is shown that commercially available fluorescent dyes, functionalized with triethoxysilane moieties, can be converted into fluorescent chemosensors by simple inclusion into silica nanostructures. Dye-doped silica nanoparticles and thin films detect Cu(II) ions in the micromolar range by the quenching of fluorescence emission. The different response toward Zn(II), Ni(II), and Co(II) metal ions was also investigated and is reported. The self-organization of the silica structures leads, at the same time, to the formation of metal ion binding sites as well as to the linking of a fluorescent reporter in their proximity. Structural features of the materials, particularly particle size and network porosity, strongly affect their ability to act as fluorescent sensors.