In this study, Pd nanoparticles were immobilized on the core–shell structure C@Fe₃O₄ (carbon is the shell and Fe₃O₄ is the core) magnetic microspheres via in situ adsorption and reduction to generate the magnetically separable Pd/C@Fe₃O₄ catalyst. In this method, no excess reductant and capping reagents were required, and it is a clean, simple and green process for the preparation of the magnetic Pd nanocatalyst. The Pd/C@Fe₃O₄ catalyst showed high activity and extraordinary stability during the oxidation of biomass derived 5-hydroxymethylfurfural (HMF) into 2,5-furandicarboxylic acid (FDCA) under mild conditions. A study aimed at optimizing the reaction conditions such as reaction temperature, reaction solvent and base amount has been performed. Under optimal reaction conditions, HMF conversion of 98.4% and FDCA yield of 86.7% were achieved after 6 h at 80 °C. After reaction, the Pd/C@Fe₃O₄ catalyst could be easily recovered by an external magnet and reused without the loss of its activity.