Branched poly(ethylene-imine) can be tagged with luminescent dyes (e.g., fluorescein isothiocyanate and tetramethylrhodamine isothiocyanate) and used to precipitate spherical silica particles from 10s-to-100s of nm diameter size under mild conditions. These dye–PEI/SiO₂ nanoparticles are highly compatible with polar solvents to give bright fluorescent suspensions, and detailed photophysical characterization reveals well-separated dye moieties with an approximately homogeneous dispersion of dye–PEI conjugate throughout the SiO₂ matrix. Reaction of PEI amine groups incorporated at the particle surface affords a simple method for post-synthesis functionalization of these materials, and the formation of FITC/Eosin-Y fluorescence resonance energy transfer pair-tagged particles and SiO₂@Au core–shell nanocomposites using this strategy is demonstrated. This bio-inspired approach to multi-functional SiO₂ nanoparticles provides a range of potential advantages over traditional “inorganic” syntheses of similar materials, as it proceeds through a scalable, single-step reaction using inexpensive reagents, enables efficient incorporation of luminescent species into the resulting particles with very limited dye aggregation, and provides nanoparticles that do not require post-synthesis modification for further conjugation with species of interest. The method offers a simple means to generate complex nanocomposites, whereby a host of desired species can be incorporated both inside and on the surface of biocompatible SiO₂ nanoparticles.