The enhanced properties of heterogeneous catalysts have led to significant interest in recent years, particularly in composite materials that incorporate organic-inorganic systems. In this particular study, a series of steps were undertaken to synthesize Fe3O4 microspheres, which were subsequently coated with chitosan and agarose. Finally, palladium nanoparticles were immobilized onto the surface of the microspheres, resulting in the formation of Fe3O4 MPs@CS-Agar/Pd NPs. To evaluate the material, advanced analytical techniques such as FT-IR, FESEM-EDS, ICP-OES, TEM, XRD, and VSM were utilized to determine its structural and physicochemical characteristics. The results shown that the Pd nanoparticles were formed in nanometer-sized particles, exhibiting a quasi-spherical shape with an average diameter ranging from 20–40 nm. Notably, the Fe3O4 MPs@CS-Agar/Pd NPs exhibited remarkable catalytic activity in Suzuki-Miyaura reaction. Importantly, the nanocatalyst could be reused up to 8 times without any decline in its activity. The exceptional catalytic performance of the Fe3O4 MPs@CS-Agar/Pd NPs in these reactions can be attributed to the distinctive nanostructure characteristics it possesses.