Abstract The significance of biogenic silicon (BSi) for Si cycling in terrestrial biogeosystems has been acknowledged since decades. Its importance originates from the fact that BSi generally is more soluble than silicate minerals and thus i) controls Si fluxes from terrestrial to aquatic ecosystems and ii) plays an important role as source of readily- or plant-available Si (i.e., H 4 SiO 4 ) in soils. In this context, physicochemical surface properties of BSi structures determine their dissolution kinetics. We applied transmission Fourier transform infrared (FTIR) spectroscopy, diffuse reflectance infrared Fourier transform (DRIFT) microscopy, and confocal laser scanning microscopy (CLSM) to investigate physicochemical surface properties of different biogenic silica structures. Using these techniques we were able to detect differences on a molecular level (FTIR, DRIFT) and in surface roughness parameters (CLSM) between BSi synthesized by protists (testate amoebae, diatoms) and BSi synthesized by plants (phytoliths) as well as between fresh (extracted from plants) and aged (extracted from soils) phytoliths. While fresh phytoliths showed organic impurities that can be assigned to occluded organic matter, aged phytoliths showed additional impurities of mineral origin. This is due to the fact that the used non-destructive gravimetric extraction of phytoliths is unsuitable for a distinct differentiation between biogenic silica (phytoliths) and non-biogenic (minerogenic or microcrystalline) Si forms in general. We recommend DRIFT microscopy for analyses of phytoliths extracted from soils because this technique allows measurements of selected, single siliceous phytoliths (as well as other BSi structures). Surface roughness parameters of aged phytoliths decreased compared to the ones of fresh phytoliths indicating a decrease of specific surface areas available for dissolution processes. Physicochemical surface properties will help us to better understand the BSi status (BSi quality and quantity) of soils with implications for Si availability in soils and thus Si cycling in terrestrial biogeosystems.