Biosensors, especially those with a SERS readout, are required for an early and precise healthcare diagnosis. Unreproducible SERS platforms hampers the clinical translation of SERS. Here we report a synthetic procedure to obtain stabile, reproducible and robust highly-SERS performing nanocomposites for labelling. We control the NPs agglomeration and codification which results in an increased number of hot spots, thus exhibiting reproducible and superior Raman enhancement. We studied fundamental aspects affecting the plasmonic thiol bond resulting in pH exhibiting a determining role. We validated their biosensing performance by designing a SERS-based sandwich immunoassay against COVID-19. The limits of detection for the recombinant SARS-CoV-2 protein is below 0.01 ng/μL. We offered herein one nanostructure with robust and homogeneous SERS signal which can be potentially applied for biodiagnosis.