Silica nanostructures are widely used as microelectronic components, catalyst supports, or drug delivery systems due to their physicochemical properties like high thermal and hydrothermal stability, optical transparency, chemical inertness, large specific surface area, and non-toxicity. All these properties predispose silica nanostructures to be used as a support for molecules or nanoparticles in various investigations. The research presented here is intended to show that silica can also be a convenient tool for studying complex molecular systems. The research concerning the magnetic and optical properties of two types of molecules will be discussed as examples. The first example is the study of the magnetic properties of molecules belonging to the single-molecule magnets group. This section will present the deposition procedures of Mn12-stearate molecules onto silica structures with controlled concentration and the magnetic properties of the systems obtained. Next, silica SBA-15 functionalized with propyl-copper-phosphonate groups will be discussed. In this section, special attention will be given to the non-linear optical properties of the materials. The presentation aims to show silica nanostructures from a new perspective as a convenient tool used for fundamental research on molecular systems.