The development of nanostructured metal-dielectric materials, suitable for biodetection based on surface plasmon resonance and surface enhanced Raman scattering (SERS), requires the refinement of proper biological protocols for their effective exploitation. In this work, the immobilization of DNA probes on nanostructured metal-dielectric/semiconductor substrates has been optimized, to develop a bioassay for the detection of miRNA. To ensure a broad relevance, the proposed biological protocol was applied to different silver-decorated functional supports: porous silicon (pSi), TiO2 nanotube arrays, and polydimethylsiloxane (PDMS). The efficiency and the stability of the substrates were carefully analyzed by Raman spectroscopy and electron microscopy after the incubation in buffers with the appropriate combination of pH, ionic strength, and surfactant content. The customized protocol, initially developed on multiwell plates, was transferred and refined on the nanostructured substrates. The nonspecific interaction of the biological species with the surface was evaluated and reduced thanks to a tailored surface pretreatment. SERS analysis was applied to check the immobilization of DNA probes on pretreated samples. Silvered PDMS-supported pSi membranes, the most promising substrates in terms of stability, were subjected to further optimizations. Concentrations, volume, and duration of incubations were finely adapted with respect to the surface probe density and to the corresponding hybridization of the complementary miRNA. The optimized ELISA-like assay shows sensitivities comparable to those of commercial plates for the detection of miRNA222 (LOD: 485 pM), paving the way for the application of the developed protocol on metal-dielectric/semiconductor nanostructures for ultrasensitive SERS biosensing applications.