Using a handheld Raman spectrometer, we demonstrate how silver nanodendritic substrates formed on microelectrode platforms can be used for ultrasensitive detection of target analytes, such as cocaine and melamine. The nanostructured substrates are formed through the electrochemical deposition of silver on electrically insulated silicon substrates with the aid of an alternating current (AC) signal applied to the microelectrodes. A nanostructure lateral growth rate of 8.90 ± 0.19 μm min-1 was achieved by implementing a semi-batch process that kept the reactant concentrations high during silver deposition. This facile process can be used with different microelectrode designs, thus allowing for customizable SERS substrates. Compared with a commercially available benchmark, our surface-enhanced Raman scattering (SERS) substrates were found to be at least twice more sensitive. Moreover, by applying multivariate analysis, specifically principal component analysis and linear classification models, the pesticide thiram was identified at 1 ppm with 100% accuracy in spiked apple juice without sample pre-processing. Our technique provides the means for combining microelectrode platforms with SERS for portable, point-of-care sensing applications.