The preponderance of methods that rely on fluorescence of an organic dye molecule for a myriad of applications leads to a general interest from the fields of biology, information technology, and security in creating bright and stable emitters.[1, 2] While many options exist to address these applications, current trends in environmental awareness and regulation of disposal are leading the field away from processes involving volatile organic compounds and materials containing toxic, heavy metals toward benign, water-based materials and processes.[3–7] One of these materials is silica, specifically sol–gel silica. Since 1968 when Stöber and coworkers first reported a polycondensation reaction of silica precursors that leads to a polymeric silica network structure for the formation of monodisperse pure silica particles, there has been an interest in using the particles for tracking, tagging, and identifying flows, cells, organs, and even barcodes.[8–10] The extensive body of research concerning the chemistry of the reaction and the many well-known ways to modify silica surfaces, has acted as a broad, solid foundation upon which to build the current research.[11–15] The particularly useful covalent incorporation of fluorescent molecules into the polymeric silica matrix, first for large silica particles and later for nanoparticles allowed for the broadened use of fluorescent nanoparticles in all of the aforementioned fields, as well as an increased understanding of how dyes are incorporated into the silica matrix.[16–21] The silica matrix has a significantly higher glass transition temperature than organic polymers, leading to improvements in the optical properties of the encapsulated dyes.[17, 22] However, for spectral multiplexing, one of the drawbacks of these