This work describes the preparation and investigation of molecularly imprinted polymer (MIP) microgel (MG) stabilized Pickering emulsions (PEs) for their ability to catalyze the formation of disulfide bonds in peptides at the O/W interface. The MIP MGs were synthesized via precipitation polymerization and a programmed initiator change strategy. The MIP MGs were characterized using DLS analysis, SEM measurement, and optical microscopy analysis. The dry and wet MIP MGs showed a hydrodynamic diameter of 100 and 280 nm, respectively. A template rebinding experiment showed that the MIP MGs bound over two times more template (24 mg g–1) compared to the uptake displayed by a nonimprinted reference polymer (NIP) MG (10 mg g–1) at saturation. Using the MIP MGs as stabilizers, catalytic oxidation systems were prepared by emulsifying the oil phase and water phase in the presence of different oxidizing agents. During the cyclization, the isolation of the thiol precursors and the oxidizing reagents nonselectively decreased the formation of the byproducts, while the imprinted cavities on the MIP MGs selectively promoted the intramolecular cyclization of peptides. When I2 was used as the oxidizing agent, the MIP-PE-I2 system showed a product yield of 50%, corresponding to a nearly 2-fold increase compared to that of the nonimprinted polymer NIP-PE-I2 system (26%). We believe the interfacial catalysis system presented in this work may offer significant benefits in synthetic peptide chemistry by raising productivity while suppressing the formation of byproducts.