In this study, new l-asparagine grafted on 3-aminopropyl-modified Fe3O4@SiO2 core–shell magnetic nanoparticles using the EDTA linker (Fe3O4@SiO2–APTS–EDTA–asparagine) was prepared and its structures properly confirmed using different spectroscopic, microscopic and magnetic methods or techniques including FT-IR, EDX, XRD, FESEM, TEM, TGA and VSM. The Fe3O4@SiO2–APTS–EDTA–asparagine core–shell nanomaterial was found, as a highly efficient multifunctional and recoverable organocatalyst, to promote the efficient synthesis of a wide range of biologically-active 3,4-dihydropyrimidin-2(1H)-one derivatives under solvent-free conditions. It was proved that Fe3O4@SiO2–APTS–EDTA–asparagine MNPs, as a catalyst having excellent thermal and magnetic stability, specific morphology and acidic sites with appropriate geometry, can activate the Biginelli reaction components. Moreover, the environmental-friendliness and nontoxic nature of the catalyst, cost effectiveness, low catalyst loading, easy separation of the catalyst from the reaction mixture and short reaction time are some of the remarkable advantages of this green protocol.