An organic sol–gel process was developed to incorporate fluorescent dyes into monodisperse melamine–formaldehyde (MF) resin microspheres. Various organic fluorescent dyes have been successfully incorporated by this process, and monodisperse fluorescent MF microspheres were prepared. Fluorescence-encoded microsphere arrays with dozens of sets were obtained by quantitatively incorporating several dyes at different doping concentrations. The characteristics and incorporating mechanism of these microspheres and their dyes were investigated by scanning electron microscopy, Malvern particle analysis, fluorescence spectroscopy, laser scanning confocal microscopy (LSCM), and flow cytometric analyses. Resonance energy transfer (RET) interactions of the doped dyes were investigated by steady-state and time-resolved fluorescence spectroscopy. The dye-incorporated microspheres were stable, and no leakage or deformation was found. With the occurrence of the RET effect among multi-doped dyes, prepared microspheres exhibited single excited, doping ratio-related emission signatures. The prepared dye-doped microspheres were coated with silica shells, which provided favorable surface properties for bioconjugate applications. This process of incorporating organic dyes could also be used to coat particles with dye-doped fluorescent MF shells. Multi-shell structured composite microspheres with fluorescent shells were also prepared by alternately repeating silica and MF coatings.