The combination of microfluidic techniques with surface-enhanced Raman scattering (SERS) microscopy provides the platform for the analysis, detection, and accurate monitoring of a wide range of analytes. Composite microparticles for SERS sensing were used here for the detection of analytes in a micro-continuous-flow arrangement. The sensor particles consisted of a swellable polyacrylamide matrix with in situ incorporated silver nanoparticles. They were prepared by a microfluidic photochemical procedure. A set of sensor particles was placed inside a glass capillary for SERS flow measurements. Highly reproducible sensor signals were observed with the test analytes adenine and histidine using a fiber-coupled compact Raman spectrometer. The particles are suited for sequential measurements under flow conditions. This could be proven by the use of a microfluidic setup with three syringe pumps for alternative actuation of different analyte and regeneration solutions.