Oxygen vacancies are prevalent in amorphous silica. It is recently recognized that the diffusion of metal cations and hydrolytic weakening at the elevated temperature produced hollow framed silica with interior voids. Electron energy-loss spectroscopy (EELS) reveals more complex behaviors of metals and oxygen underneath this seemingly simple shape evolution. In Fe 3 O 4 /SiO 2 nanocomposites, polyhedral distortion is severe, and the alteration of Si−O− Si bonding occurs. Ionic character is strengthened, and the oxidation number of Si decreases with increasing annealing temperature. Despite this distortion, ordering of oxygen within amorphous silica is enhanced with the increase of annealing temperature. Reduction of Fe 3+ to Fe 2+ is also facilitated by the diffusion of Fe 3+ into SiO 4 tetrahedra. In the presence of Co, however, polyhedral distortion is not severe, and it is supposed that Co not only resides on the surface of mesoporous silica but also inhibits the diffusion of Fe into SiO 4 tetrahedra. In addition, Co suppresses the formation of Fe 3 O 4 and other iron oxides, and it also retards the formation of CoFe 2 O 4 . Despite the shape reorganization in CoFe 2 O 4 /SiO 2 nanocomposites, the covalent nature of SiO 4 tetrahedra is maintained throughout the annealing temperature. Under the slow heating process (2.5 °C/min), however, the diffusion of Fe and Co is enhanced, and they undergo amorphous alloying with Si. Without making crystalline CoFe 2 O 4 , this alloying contributes to the formation of metallic Si. All these observations are governed by oxygen deficiency in amorphous silica and the enhanced diffusion of transition metal cations at the elevated temperature.