In this work, we report a simple and effective approach for preparing molecular imprint polymer (MIP) coatings directly on magnetic multicore (MMC) iron oxide nanoparticles using a microwave reactor to trigger the polymerization reaction. The nanoparticles were manufactured using a microwave reactor, and the MIPs were synthesized with rhodamine 6G (R6G) as the template molecule, methacrylic acid as the functional monomer, and ethylene glycol dimethacrylate as the cross-linker. The produced MMCs and MMC-MIPs were extensively characterized by analysis of powder X-ray diffraction data, Fourier transform infrared spectra, Mossbauer spectroscopy, SQUID magnetometry, and transmission electron microscopy (TEM). The results show the effective formation of the polymeric layer on the surface of the MMCs, without alteration of the structure or physical properties of the core magnetic nanoparticles. The synthesized MIPs presented a high efficiency in the imprinting process of the MMC-MIPs and high selectivity (MIP R6G, Ka = 7.31 × 10–2 M–1 y, 𝑁¯= 14.14 μmol g–1) toward the target molecule R6G.