Organic-inorganic silicon-based polymers can be tailor-made to obtain materials with mechanical, chemical, optical, or electric properties that suit a great variety of applications and are compatible with microfabrication technologies. Herein, this work reports on the one-step processing of microstructures of a sol-gel polymeric material on flat substrates by microtransfer molding. A careful selection of silanes and the experimental conditions for the generation of the three-dimensional polymeric network was of key importance to obtain structures of up to 70 μm high having an aspect ratio of up to 10:1 (height/width), with excellent periodicity and reproducibility. Besides, a very low degree of shrinkage of the sol-gel polymer was shown upon aging and drying steps, thereby enabling the perfect control over the fabrication of the final structure. Pillars, wells, and lines of different dimensions were fabricated and characterized by optical, scanning electron, and atomic force microscopy techniques. The controlled development of sol-gel microstructures using a simple fabrication technology may widen the range of promising applications of these materials in areas such as optoelectronics or chemical sensing.