We demonstrate the enhanced analytical sensitivity of both surface enhanced Raman scattering (SERS) and surface enhanced resonance Raman scattering (SERRS) responses, resulting from the in situ synthesis of silver colloid in a microfluidic flow structure, where both mixing and optical interrogation were integrated on-chip. The chip-based sensor was characterized with a model Raman active label, rhodamine-6G (R6G), and had a limit of detection (LOD) of ca. 50 fM (equivalent to single molecule detection). The device was also used for the determination of the natural pigment, scytonemin, from cyanobacteria (as an analogue for extraterrestrial life existing in extreme environments). The observed LOD of approximately 10 pM (ca. <400 molecules) demonstrated the analytical advantages of working with freshly synthesized colloid in such a flow system. In both cases, sensitivities were between 1 and 2 orders of magnitude greater in the microfluidic system than those measured using the same experimental parameters, with colloid synthesized off-chip, under quiescent conditions.