In utilizing the exceptional optical properties of metallic nanoparticles, surface enhanced Raman spectroscopy (SERS) is an excellent candidate for analytical detection schemes due to its molecular specificity and high sensitivity. To record reliable SERS signals, impurifications on the metallic surface contributing to the overall SERS signal, have to be removed. In this context, it is important to improve the nanostructures’ quality to implement SERS in routine analytical applications. Here, we report about an easy to handle and fast protocol for the generation of SERS active nanoparticles by enzymatically reducing silver ions to their elementary state and oxidizing hydroquinone (HQ) to p-benzoquinone (p-BQ). However, these SERS substrates lead to a strong background signal overlapping with the actual analyte Raman bands. In order to quench this background signal and to protect the silver nanoparticles from oxidation we covered metallic nanoparticles with a dielectric layer of alumina (Al2O3) by applying plasma enhanced atomic layer deposition (PE-ALD). This coating guarantees the stability of these SERS substrates for at least 4 weeks after preparation under ambient storing conditions. The sensitivity of these enzymatically generated nanoparticles (EGNPs) coated with a 1 nm Al2O3 layer allows for a background free detection of riboflavin down to less than 10 nM. Furthermore, the improved specificity of these background-free and bottom-up produced plasmonic arrays has also been demonstrated by detecting a retinol monolayer.