A novel approach for molecularly imprinting proteins, i.e. inhibitor-assisted imprinting, onto silica microspheres is discussed, which provides advanced functional materials addressing prevalent challenges in the field of protein purification and isolation from biotechnologically relevant media. Pepstatin-assisted surface-imprinted core-shell microbeads for the acidic protease pepsin were synthesized serving as selective sorbent material for solid phase extraction (SPE) applications. The inorganic core, i.e., amino-functionalized silica spheres (AFSS), is prepared by co-condensation of tetraethylorthosilicate (TEOS) and (3-aminopropyl) trimethoxysilane (APTMS) in water-in-oil (W/O) emulsion, which is then reacted with pepstatin, a selective inhibitor of pepsin, onto the surface of the AFSS via an amide bond. 3aminophenylboronic acid (APBA) serves as the functional monomer for establishing nanothin imprinted polymer films, i.e., poly (3-aminophenylboronic acid) (pAPBA) at the surface of the pepstatin-immobilized AFSS via oxidation by ammonium persulfate in aqueous solution in the presence (molecularly imprinted polymer, MIP) and absence (non-imprinted polymer; NIP) of pepsin. Thus obtained core-shell microbeads are packaged into SPE cartridges for evaluating the selectivity for pepsin. Each individual synthesis step is thoroughly characterized using x-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and BET methods. Finally, the imprinted core-shell microbeads indeed provide specific binding.