In this work, a novel molecularly imprinted stir-bar was developed for the stir-bar sorptive extraction (SBSE) of thiabendazole (TBZ) and carbendazim (CBZ) from orange samples. Magnetic nanoparticles were surface modified with oleic acid and then encapsulated by a silica shell using a conventional sol-gel procedure. Subsequently, nanoparticles were functionalized with methacrylate functionalities by grafting onto the particles surface. Finally, the modified magnetic nanoparticles were entrapped in a polymer monolith synthetized by copolymerization with the imprinting polymerization mixture using a glass vial insert as a mold. Variables affecting the polymerization and rebinding conditions of target analytes were optimized. The uptake capacity for the template (TBZ) was evaluated as well as the cross-reactivity for the related compound CBZ by rebinding experiments. Finally, the proposed magnetic imprinted monolith was applied to the SBSE of TBZ and CBZ from orange sample extracts providing a remarkable clean-up ability. The calculated detection limit were 0.13 and 0.10 mg kg−1 for CBZ and TBZ respectively, low enough to satisfactory analysis of both compounds in orange samples according to current European Union regulations. Display omitted •A stir-bar based on an imprinted monolith polymer containing magnetic nanoparticles is developed.•MIP magnetic stir-bar for the stir-bar sorptive extraction of thiabendazole and carbendazim was studied.•Thiabendazole and carbendazim were successfully extracted from orange sample extracts.