Immunomagnetic separation (IMS) beads with antibody coating are an interesting option for biosensing applications for the identification of biomolecules and biological cells, such as bacteria. The paramagnetic properties of the beads can be utilized with optical sensing by migrating and accumulating the beads and the bound analytes toward the focus depth of the detection system by an external magnetic field. The stability of microbial detection with IMS beads was studied by combining a flexible, inexpensive, and mass producible surface-enhanced Raman spectroscopy (SERS) platform with gold nanoparticle detection and antibody recognition by the IMS beads. Listeria innocua ATCC 33090 was used as a model sample and the effect of the IMS beads on the detected Raman signal was studied. The IMS beads were deposited into a hydrophobic sample well and accumulated toward the detection plane by a neodymium magnet. For the first time, it was shown that the spatial stability of the detection could be improved up to 35% by using IMS bead capture and sample well placing. The effect of a neodymium magnet under the SERS chip improved the temporal detection and significantly reduced the necessary time for sample stabilization for advanced laboratory testing.