Facile synthesis of silica-based functional materials at low temperatures has remained a challenge in materials science. To this end, we demonstrate the use of a gaseous ozone stream, generated via an electric discharge method, as a versatile tool for the postsynthesis modification of silica-based functional nanomaterials. First, a parametric study is conducted with a mesoporous model material to obtain basic insights into the reaction of the organics with ozone. The study is then extended to a number of distinct silica-based inorganic materials. The scope of ozone treatment can be broadly classified into three categories: (a) elimination of templates or structure directing agents (SDAs) from materials with pore sizes ranging from 0.5 to 10 nm, (b) selective transformation of organic groups functionalized on the mesoporous silica, and (c) simultaneous elimination of intermediate polymeric shells and template from the outer shells to obtain yolk−shell type materials. Each material studied here requires different parameters (temperature, time, and concentration of ozone) depending on its physical and chemical properties which have been carefully examined. Overall, the study demonstrates the potential of ozone treatment in tailoring functional materials at low temperature and provides vital insights into the reaction of ozone with silica-based materials. The study shows that gaseous ozone treatment is not limited to only one type of materials but can be applied to many systems, and we are convinced that the methodology can be applied to a multitude of organic@inorganic systems way beyond the scope of materials presented here.