This work reports on an effective approach for the continuous synthesis of Ag–Au nanoparticles (NPs) by integrating low-temperature plasma with a microfluidic technique. Crystalline Ag–Au nanoalloys are demonstrated to be produced, and the composition of the nanoalloys can be effectively tuned in-flight by controlling the concentrations or the flow rates of the reactants. The surface-enhanced Raman scattering (SERS) properties of the NPs are further validated through the detection of rhodamine 6G and crystal violet (CV) analytes. The silicon substrates coated with the Ag–Au NPs have reproducible morphology and thickness, and can significantly enhance the Raman signals, where nanoalloys show much higher Raman responses compared to monometallic Ag and Au NPs. The Ag–Au-functionalized SERS platforms show excellent reproducibility and stability, with the detection limits of 10–8 and 10–10 M for the rhodamine 6G (R6G) and CV molecules, respectively. These results indicate that the developed microfluidic plasma method is promising for the continuous and in-flight synthesis of tunable monometallic or multimetallic nanoparticles.