For centuries, humans have relied on natural products to prevent and treat numerous health issues. However, biologically active compounds from natural sources, such as polyphenols, face significant challenges, including low solubility, rapid metabolism, and instability, which hinder their effectiveness. Advances in science and nanotechnology have provided solutions to overcoming these problems through the use of porous silica materials. These materials possess unique properties, such as a high specific surface area, adjustable particle and pore sizes, and a surface that can be easily and selectively modified. In this review, we summarize and discuss findings on how the pore and particle size, structure, and surface modification of silica materials influence the preparation of efficient delivery systems for biologically active polyphenols from natural sources. The available data demonstrate how parameters such as adsorption capacity, release and antioxidant properties, bioavailability, solubility, stability, etc. of the studied delivery systems could be affected by the structural and chemical characteristics of the porous silica carriers.