This work describes the straightforward synthesis of a novel heterogeneous palladium catalyst immobilized on magnetic Janus-type silica particles coated with an amphiphilic ionic liquid (IL) layer. The material was prepared via a one-pot process wherein TEOS (tetraethoxysilane) and a bis(triethoxysilane) IL precursor are combined to form hollow shells. The IL motifs are selectively located on the outer surface of the hollow particles and serve as centers for the immobilization of palladium species on the material’s surface. The outer surface also hosts magnetic nanoparticles in close proximity to the palladium sites. Thanks to the uniform coverage of the surface with the amphiphilic IL functionality, the material exhibits a well-balanced wettability with reaction components of different polarities. The catalyst’s activity was tested in the Sonogashira cross-coupling reaction of terminal acetylenes and iodobenzene derivatives in water as the solvent. The results show that the mixed palladium–iron oxide catalyst exhibits higher activity than materials containing either immobilized palladium or iron oxide alone, suggesting a synergistic effect in this reaction. Additionally, the reaction proceeds well in the absence of expensive organic ligands and commonly employed additives such as copper co-catalysts or phase transfer catalysts. Furthermore, the material was also used in the oxidative Sonogashira coupling reaction of phenylboronic acid and phenylacetylene. The catalyst can be easily separated using an external magnet and can be reused several times. The feasibility of producing diphenylacetylene on a gram scale via the Sonogashira cross-coupling reaction was also investigated.