In this project, the main aim is the design and present a novel and unique heterogeneous nanocatalyst based on a metal–organic framework/covalently sulfonated magnetic SBA-15 mesoporous silica composite with the emphasis on promoting clean and green synthetic transformations and increasing the catalytic properties. In more detail, initially, SBA-15 containing magnetic nanoparticles was functionalized by a 1,3-propane sultone ligand. In the next step, the functionalized mesoporous substrate was used as a scaffold for the growth and synthesis of the zeolite imidazolate framework-8 (ZIF-8) crystals. The obtained composite was further applied as a suitable support for the immobilization of Pd nanoparticles via a post-modification procedure and the generation of heterogeneous catalysts. The prepared Fe3O4@SBA-15-SO3H@ZIF-8@Pd was incorporated as a heterogeneous and green catalyst in the Suzuki coupling reaction in the natural deep eutectic solvent with efficient recyclability.