We demonstrate a synthetic strategy toward functional, composite porous materials by incorporating functionalized porous silica spheres into a hierarchically porous silica matrix. Monodisperse mesoporous silica spheres decorated with organic probe molecules for visual Cd2+ ion detection were coated with a thin protecting poly(methyl methacrylate) (PMMA) layer to form core-shell particles. When these particles were redispersed in a mixture of a silica precursor, surfactant and hydrochloric acid, hierarchically structured composite films could be prepared by spin-coating and aging. The PMMA capsule protected the mesoporous silica spheres from being exposed to the silica precursor in the assembly step, which could have blocked the mesopores and/or reacted with the surface functional species. Once the polymer and surfactant components were removed by extraction while preserving the organic probe molecules within the silica spheres, composite porous structures were derived in which the mesoporous silica spheres were surrounded by a skeleton of another mesoporous silica phase. An observed color change of the film after exposure to analyte solutions with low concentrations of Cd2+ ions confirmed that the confined probe molecules remained active after the multiple processing steps and that they were accessible via the mesopores in the silica matrix surrounding the embedded spheres. By separating the sphere synthesis and functionalization steps from the film casting step, it is possible to choose different pore-forming surfactants during the syntheses of the spheres and the matrix, and in principle, to embed multiple sets of mesoporous spheres with different functional groups, whose syntheses may not be compatible with each other.