Multifunctional particles with combined magnetic and optical properties are promising materials for applications such as sensing and detection of analytes, and contrast agents for imaging techniques such as MRI, and photocatalysis. While the magnetic property allows for non-contact manipulation of the nanoparticles, optical properties can be harnessed for such sensing applications. We present the synthesis and large-scale assembly of inter-layered magnetic-plasmonic nanoparticles with graphene oxide (GO) spacer (Fe3O4@GO@Ag). The multifunctional composite particles were prepared using simple chemical methods and had an average size of 220 nm. The prepared samples were characterized using different techniques including powder XRD, FT-IR, Raman scattering, SEM and TEM imaging. By using an external magnetic field, it is possible to form an assembly of these multifunctional particles on a large scale. Due to the chain-like formation in the presence of a magnetic field, such assemblies are good substrates for surface-enhanced Raman scattering (SERS). Here, we demonstrate the application of these magnetically assembled-particles for the detection of very low concentrations of analyte molecules (4-mercaptopyridine) using SERS. These multifunctional composite particles are good candidates for potential applications involving chemical detection, photocatalytic reactions, optoelectronic devices, and photothermal effects.