Phytoestrogens daidzein (4',7-dihydroxy-isoflavone) and formononetin (4'-methoxy-7-hydroxy-isoflavone) have been studied by surface-enhanced Raman (SER) spectroscopy. Spectra were acquired in the presence of citrate-reduced silver colloids, over a range of pH and concentrations. Density functional theory calculations were used to assist assignment of the normal Raman spectra and help determine the mode of interaction of isoflavones with the silver nanoparticles. Formononetin does not show SER activity unless the 7-OH group is deprotonated, and accordingly, the interaction with the silver surface occurs via the deprotonated site. Daidzein, on the other hand, appears to contain multiple species at the surface, interacting via both the hydroxyl groups at 7-OH and 4'-OH, after deprotonation. This is an important result that points to potential future SERS applications in phytoestrogen analysis and provides a foundation for understanding the SER spectra of isoflavones.