Folic acid is an essential nutrient involved in biosynthetic processes and cell growth. From an analytical point of view, folic acid can be used as an active part of sensors for substances with affinity to folic acid molecules. In biological environment, sensors can be exposed to temperatures that differ from room temperature. Thus, it is important to describe the influence of temperature on adsorbed molecules, especially on orientation of molecules towards the metal surface and on stability of adsorbed layer. Surface-enhanced Raman scattering spectroscopy is a useful tool for investigation of architecture of molecular layers adsorbed on metal surfaces because the spectral features change with varying orientation of molecules towards the surface, as well as with changes in interactions among adsorbed molecules. In this study, folic acid was adsorbed on electrochemically prepared Au and Ag substrates, and both these substrates were exposed to temperature changes according to the temperature program consisting of stabilization, the substrate temperature at 10°C, at 50°C and back at 10°C. Decomposition of adsorbed folic acid at 50°C can be excluded on both metals, though the metal (Ag or Au) influences the arrangement of adsorbed molecules and its temperature-induced changes. In the case of Ag substrate, significant and irreversible increase of certain Stokes band intensities is observed, whereas in the case of Au substrate, the band intensity increase is negligible. Experimental spectra were analyzed using principal component analysis and supplemented with calculated data for folic acid molecule adsorbed on small metal cluster using density functional theory. Moreover, it was proved that changes of surface plasmon resonance and collision frequency of Ag substrate are negligible in the studied temperature interval. Slight re-orientation of adsorbed folic acid molecules was identified as the main source of band intensity variation in the spectra of folic acid adsorbed on Ag. Copyright © 2014 John Wiley & Sons, Ltd.