Multifunctional mesostructured silica microspheres are prepared using ultrasonic aerosol spray in conjunction with solvent evaporation-induced assembly. Rare earth ion–phenanthroline complexes, magnetite particles, photoacid generators, and pH-sensitive dyes are chosen as luminescent, magnetic, and photosensitive components. The incorporation of these functional components into mesostructured silica microspheres can be readily realized by dispersing them in the precursor solution of the aerosol spray process. Luminescent microspheres that can emit at multiple wavelengths when excited at a single wavelength are produced by the addition of multiple rare earth complexes into the precursor solution. The addition of magnetite particles leads to the production of magnetic luminescent microspheres. Photoacid generators and pH-sensitive dyes are further employed to produce magnetic photosensitive microspheres that can release acid and change color upon UV light illumination. Such multifunctional microspheres could have exciting potential for many optical and biotechnological applications, such as multiplexed labeling, diagnosis, simultaneous imaging and therapy, cell capture and separation, targeted delivery, and optical data storage.