Morphological transformation was performed on Stöber silica nanospheres (ca. 270 nm in diameter) and transmuted into either ZnSiO (zinc silicate) nanoflowers or MgSiO (magnesium silicate) nanoflowers (600–800 nm in diameter) through a facile hydrothermal process. The zinc silicate materials were then chosen for incipient wetness impregnation to imbue them with different levels of Cu and Zn doping due to the well-established elemental synergy of Cu and Zn toward methanol synthesis via CO2 hydrogenation. Characterization results concur that zinc silicate nanoflowers loaded with copper(II) oxide were formed after incipient wetness impregnation. Three as-synthesized catalyst candidates with different copper loadings were then evaluated for CO2 hydrogenation and compared against an industrial catalyst. After the reaction, high-resolution transmission electron microscopy (HRTEM) with energy-dispersive X-ray (EDX) elemental mapping reveal that petite Cu nanoparticles formed on the petals of the impregnated zinc silicate nanoflowers. Experimental results show that all catalyst materials have an exceptional high methanol selectivity, with overall performance exceeding that of the industrial catalyst at per Cu basis. Both ZnSiO and MgSiO were also evaluated through a simple methylene blue adsorption test. Hence, through deliberate morphological control and chemical transformation, superficially inert Stöber silica nanospheres were functionalized into transition- and earth-alkaline metal silicates, which exhibit catalytic and adsorptive properties with a nanoflower morphology that prevents interstacking of nanosheets.