Aggregated metal nanoparticles exhibit enhanced localized electromagnetic fields that enable highly sensitive vibrational spectroscopy analysis based on surface-enhanced Raman scattering (SERS). We demonstrate SERS detection of organic analytes adsorbed to optically aggregated silver nanoparticles in a microfluidic device. The combination of optical tweezers and microfluidics technologies paves the way for novel lab-on-a-chip based plasmonic chemo/bio sensors and overcomes two important drawbacks of standard SERS sensing schemes; i.e. the renewal of nanofabricated metallic substrates and the difficulty of avoiding uncontrolled aggregation in metal colloids.