Creation of structural complexity by simple experimental control will be an attractive approach for the preparation of nanomaterials, as a classical bottom-up method is supplemented by a more efficient and more direct artificial engineering method. In this study, structural manipulation of MCM-41 type mesoporous silica is investigated by generating and imbedding hard magnetic CoFe2O4 nanoparticles into mesoporous silica. Depending on the heating rate and target temperature, mesoporous silica undergoes a transformation in shape to form hollow silica, framed silica with interior voids, or melted silica with intact mesostructures. Magnetism is governed by the major CoFe2O4 phase, and it is affected by antiferromagnetic hematite (α-Fe2O3) and olivine-type cobalt silicate (Co2SiO4), as seen in its paramagnetic behavior at the annealing temperature of 430 °C. The early formation of Co2SiO4 than what is usually observed implies the effect of the partial substitution of Fe in the sites of Co. Under slow heating (2.5 °C min(-1)) mesostructures are preserved, but with significantly smaller mesopores (d100 = 1.5 nm). In addition, nonstoichiometric CoxFe1-xO with metal vacancies at 600 °C, and spinel Co3O4 at 700 °C accompany major CoFe2O4. The amorphous nature of silica matrix is thought to contribute significantly to these structurally diverse and rich phases, enabled by off-stoichiometry between Si and O, and accelerated by the diffusion of metal cations into SiO4 polyhedra at an elevated temperature.