Biosilification is of interest due to its capability to produce a highly intricate structure under environmentally friendly conditions. Despite the considerable effort that has been devoted toward biomimetic silification, the synthesis of highly complex silica structures, as found in the structures of diatom cell walls, is still in its infancy. Here, we report the bioinspired fabrication of well-organized and symmetric silica nanostructured networks, involving phase separation and silicic acid polymerization processes, in analogy to the morphogenesis of diatom cell walls. Our approach exploits self-assembled silica spheres as a self-source of the silicic acids as well as scaffolds that, interplayed with droplets of ammonium hexafluorosilicate, direct the site-specific silification. Moreover, we have achieved multiple morphological evolutions with subtle changes in the process, which demonstrates exquisite levels of control over silica morphogenesis.