Temporal changes in signal intensity of Surface Enhanced Raman Scattering (SERS) upon laser excitation is an interesting phenomenon in plasmonics. In-depth understanding of the phenomena is highly important especially when developing a SERS sensor based on the intensity variation of particular Raman peak/band. One of the main challenges in such a technique is the intensity reduction at a given location upon consecutive measurements. Previously, signal loss in SERS measurement was attributed to the electric-field induced roughness relaxations in the SERS active surface. In such cases, as the surface is smoothened out, signals are completely lost. In our observation, the reduction in the spectral intensity is irreversible but never completely lost and a major part of it can be attributed to the plasmon induced heating effect. Here, we experimentally demonstrate this effect by studying the SERS signal from four different Raman active molecules adsorbed onto substrates that contain uniform nano-roughened bi-metallic silver/gold coating. Possible mechanism that leads to irreversible signal loss is explained. Moreover, solutions for minimising such plasmonic heating when developing a biosensor are also discussed. © 2009 SPIE.