The synthesis of doubly ordered core-shell silica based microspheres showing different ordered mesoporous arrangements in core and shell was described. Core mesoporous microspheres were made using an aerosol-assisted process in the presence of nonionic surfactant and the mesoporous shells encapsulating the core microspheres were added to the materials. Some isolated MCM-41 type microspheres could be observed after the shell formation by the Stöber method, most of the material resulting from the synthetic procedure. High resolution scanning electron microscopy (HRSTM) images show that the core and shell mesoporous components appear to be connected through a columnar interface, which can be distinguished between the mesoporous phases. The surface of the silica core is negatively charged during the shell synthesis, showing that the cationic molecules would create a layer over the surface of the core microspheres.