Imaging of chemical composition in microfluidic chips is addressed using Surface Enhanced Raman Spectroscopy (SERS). The Y-shaped SERS microfluidic chip used is fabricated by xurography and an electrodeposition method is employed to form a thin nanostructured silver layer over the bottom glass wall of the main microchannel. Used as an immobilized SERS substrate, this layer of silver nanocrystals exhibits an analytical enhancement factor of 5.104 uniformly distributed over its surface (RSD < 7%). These good performances allow the quantitative imaging of transverse diffusion profiles of Crystal Violet (CV) at low concentrations (10-8-10-6 mol/L). The SERS measurement turns out to be reversible at high laser power and this is explained by the thermal desorption of adsorbed CV (photothermal effect). However, too high heating leads to a low amount of adsorbed species and a low SERS signal. This effect is limited by using a fast enough flow inducing a cooling effect. A compromise must be found between laser power and liquid flow rate to enable a reversible and sensitive SERS measurement in the chip. These findings should contribute to the development of imaging, in microfluidic conditions, of the spatiotemporal dynamics of weakly concentrated key molecules involved in chemical, biochemical or biological processes.