Here we demonstrate a facile, two step formation of silver core - gold shell (Ag–Au) nanostructures using microelectrodes and assess their performance as surface-enhanced Raman scattering (SERS) substrates to detect and quantify toxicants. Ag nanostructures, serving as the scaffolds for the bimetallic structures, were grown first by using electrochemical deposition on the edges of microelectrodes functionalized with the alkanethiol, 11-mercaptoundecanoic acid. Subsequently, different concentrations of HAuCl₄ were used to perform a galvanic reaction on the surfaces of the Ag nanostructures with aqueous droplets being placed on the microelectrodes for 10 min before the substrate was rinsed and dried. Lower HAuCl₄ concentrations were found to better preserve the fractal morphology of the formed Ag–Au nanostructures, while higher concentrations resulted in Ag–Au fragments. The SERS enhancement factor for the Ag–Au nanostructures was estimated to have a max value of 6.51 x 10⁵. Combining a data reduction technique with a linear classifier, both identification and quantification were demonstrated with 100% success. The toxicants thiram, thiabendazole, malachite green and biphenyl-4-thiol were all detected and identified at 1 ppm. Lastly, as a proof of concept, the Ag–Au nanostructures were transferred to a PDMS film resulting in a flexible SERS substrate capable of direct detection of thiram on an apple peel without any additional sample pre-treatment.