In this study, a core-shell type synthetic protein scavenger material was developed for selectively binding pepsin using an inhibitor-assisted molecular imprinting strategy. Pepstatin (an inhibitor of pepsin) was immobilized onto the surface of amino polystyrene (APS) microbeads via a carbodiimide linker reaction. 3-Aminophenylboronic acid (APBA) was used as a functional monomer, and poly(3-aminophenylboronic acid) (pAPBA) prepared in the presence (molecularly imprinted polymer; MIP) and absence (non-imprinted polymer; NIP) of the pepsin template was then successfully grafted onto the surface of the pepstatin-immobilized APS microbeads via aromatic ring electron-pairing interactions in aqueous medium. After extraction of the template, pepsin binding sites at or close to the surface of the microbeads were apparently generated. Good fitting of experimental results to the Langmuir isotherm confirmed the existence of homogeneous pepsin binding sites on the surface of the imprinted microbeads. In addition, a selectivity study performed using pepsin, papain, trypsin and thermolysin proteins proved the high affinity of the core-shell microbeads to the pepsin template. The resulting remarkable imprinting factor () of 1.90 along with exceptionally high binding capacity (19.0 mg pepsin per g) confirmed that pepsin was effectively imprinted onto the surface of APS microbeads, thus providing a practically useful scavenger material applicable, for example, in biotechnologically relevant clean-up processes.