AbstractAn innovative approach for molecularly imprinting proteins, i. e., inhibitor‐assisted imprinting was used for addressing the major challenge of protein purification from biotechnologically relevant media. Pepstatin‐assisted pepsin surface‐imprinted microbeads were synthesized as a selective sorbent for solid phase extraction (SPE). The amino‐functionalized porous core was prepared by co‐condensation and post‐grafting strategies. The immobilized inhibitor pre‐organizes the template pepsin with a defined orientation prior to imprinting ensuring enhanced efficiency of the imprinting process. 3‐aminophenylboronic acid (APBA) was used as a functional monomer establishing organic nanoscale films comprising poly(3‐aminophenylboronic acid) (pAPBA) within the pores of the beads in the presence (MIP) and absence (NIP) of pepsin. Next to a detailed characterization of these advanced functional hybrid materials it was demonstrated that such porous surface‐imprinted core/shell beads feature exquisite selectivity for pepsin during individual protein rebinding studies, and more importantly, during competitive rebinding studies in protein mixtures.