The surface of Fe3O4@SiO2 nanoparticles was modified using l‐arginine as a green and available amino acid to trap palladium nanoparticles through a strong interaction between the metal nanoparticles and functional groups of the amino acid. The proposed green synthetic method takes advantage of nontoxic reagents through a simple procedure. Characterization of Fe3O4@SiO2@l‐arginine@Pd(0) was done using Fourier transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, energy‐dispersive X‐ray spectroscopy, X‐ray diffraction, vibrating sample magnetometry and inductively coupled plasma analysis. The catalytic activity of Fe3O4@SiO2@l‐arginine@Pd(0) as a new nanocatalyst was investigated in C–C coupling reactions. Waste‐free, use of green medium, efficient synthesis leading to high yield of products, eco‐friendly and economic catalyst, excellent reusability of the nanocatalyst and short reaction time are the main advantages of the method presented. Copyright © 2016 John Wiley & Sons, Ltd.