In this work, we developed a core–shell nanostructured magnetic composite by functionalizing layered double hydroxide (Mg-Al-LDH) microspheres with Fe3O4@SiO2, for the recovery of Au(III) and Pd(II). The magnetic Fe3O4 nanoparticles provided effective magnetic separation of the adsorbent from aqueous solutions. While silica protected the Fe3O4 nanoparticles, increased the adsorption sites and the stability of the material. Finally, Mg-Al-LDH was chosen because of its large anion sorption capacities which lead to the improved adsorption capacity of Fe3O4@SiO2@ Mg-Al-LDH nanocomposite. The morphology and structural composition of the nanocomposite were characterized using various analytical techniques. It was satisfactorily established that silica was coated on iron oxide and layered double hydroxide was immobilized on Fe3O4@SiO2. Parameters affecting adsorption of the composite towards Au(III) and Pd(II), such as effects of sample pH, mass of adsorbent, extraction time, eluent type and concentration were investigated using response methodology based on central composite design. Maximum adsorption capacities of Fe3O4@SiO2@ Mg-Al-LDH for Au(III) and Pd(II) were 289 mg g−1 and 313 mg g−1, respectively. Under optimum conditions, the proposed method displayed good analytical performance suggesting that the adsorbent is a good candidate for quantitative extraction of Au(III) and Pd(II) from secondary sources. Additionally, %recoveries ranging from 85%–99.6% were obtained revealing that Fe3O4@SiO2@ Mg-Al-LDH could selectively extract Au(III) and Pd(II) from leaching solutions of SARM 107 PGM ore and SARM 186 PGM concentrate.