Surface-enhanced Raman scattering (SERS) is often impaired by the limited affinity of molecules to plasmonic substrates. Here, we use carbon fiber microelectrodes modified with silver nanoparticles as a plasmonic microsubstrate with tunable affinity for enrichment and molecular identification by SERS. The silver nanoparticles self-assemble by electrostatic interaction with diamine molecules that are electrochemically grafted onto the surface of the microelectrodes. β-carotene and trans-β-Apo-8'-carotenal, producing similar resonant SERS spectra, are employed as model molecules to study the effect of electroenrichment and SERS screening for different electrode potentials. The data show that at a characteristic electrode potential, the low affinity of polyene chains without hydrophilic groups to the substrate can be overcome. Different potentials were applied to recognize the two types of carotenoids by their typical SERS signal, and the applicability of this strategy was further confirmed in the environment of a real cell culture. The results indicate that by regulating the potential, carotenoid molecules with a similar molecular structure can be selectively quantified and identified by SERS. The developed SERS-active microelectrode is expected to help the development of portable, miniaturized point-of-care diagnostic SERS sensors.