Molecular imprinting technology is a well-known strategy to synthesize materials with a predetermined specificity. For fifty years, the “classical” approach assumed the creation of “memory sites” in the organic polymer matrix by a template molecule that interacts with the functional monomer prior to the polymerization and template removal. However, the phenomenon of a material’s “memory” provided by the “footprint” of the chemical entity was first observed on silica-based materials nearly a century ago. Through the years, molecular imprinting technology has attracted the attention of many scientists. Different forms of molecularly imprinted materials, even on the nanoscale, were elaborated, predominantly using organic polymers to induce the “memory”. This field has expanded quickly in recent years, providing versatile tools for the separation or detection of numerous chemical compounds or even macromolecules. In this review, we would like to emphasize the role of the molecular imprinting process in the formation of highly specific siloxane-based nanomaterials. The distinct chemistry of siloxanes provides an opportunity for the facile functionalization of the surfaces of nanomaterials, enabling us to introduce additional properties and providing a way for vast applications such as detectors or separators. It also allows for catalyzing chemical reactions providing microreactors to facilitate organic synthesis. Finally, it determines the properties of siloxanes such as biocompatibility, which opens the way to applications in drug delivery and nanomedicine. Thus, a brief outlook on the chemistry of siloxanes prior to the discussion of the current state of the art of siloxane-based imprinted nanomaterials will be provided. Those aspects will be presented in the context of practical applications in various areas of chemistry and medicine. Finally, a brief outlook of future perspectives for the field will be pointed out.