Abstract The dynamics of cyanobacterial silicification was investigated using synchrotron-based Fourier transform infrared micro-spectroscopy. The changes in exo-polymeric polysaccharide and silica vibrational characteristics of individual Calothrix sp. filaments was determined over time in a series of microcosms in which the microbially sorbed silica or silica and iron load was increased sequentially. The changes in intensity and integrated area of specific infrared spectral features were used to develop an empirical quantitative dynamic model and to derive silica load-dependent parameters for each quasi-equilibrium stage in the biomineralization process. The degree of change in spectral features was derived from the increase in integrated area of the combined silica/polysaccharide region (Si-O/C-O, at 1150–950 cm −1) and the Si-O band at 800 cm −1, the latter representing specific silica bonds corresponding to hydrated amorphous SiO 4 tetrahedra. From the degree of change, a two-phase model with concurrent change in process was derived. In the first phase, a biologically controlled increase in thickness of the exo-polymeric polysaccharide sheath around the cell was observed. In phase two, a transition to an inorganically controlled accumulation of silica on the surface of the cyanobacterial cells was derived from the change in integrated area for the mixed Si-O/C-O spectral region. This second process is further corroborated by the synchronous formation of non-microbially associated inorganic SiO 4 units indicated by the growth of the singular Si-O band at 800 cm −1. During silicification, silica accumulates (1) independently of the growth of the sheath polysaccharides and (2) via an increase in chain lengths of the silica polymers by expelling water from the siloxane bonds. IR evidence suggest that an inorganic, apparently surface catalyzed process, which leads to the accumulation of silica nanospheres on the cyanobacterial surfaces governs this second stage. In experiments where iron was present, the silicification followed similar pathways, but at low silica loads, the iron bound to the cell surfaces slightly enhanced the reaction dynamics.