The immobilization of silica and iron by the bacteria Bacillus subtilis was monitored in controlled microcosms to elucidate the role iron may play in aiding bacterial silicification in hot springs. Silica and iron immobilization was monitored as a function of bacterial concentration, iron concentration, and silica concentration (both undersaturated and oversaturated with respect to amorphous silica). Results demonstrate that bacterial cells do immobilize more Fe than bacteria-free systems in solutions with iron concentrations ≤50 ppm Fe. However, as iron concentrations increase, the difference between Fe immobilization in bacterial and bacteria-free systems decreases as non-bacterially mediated precipitation processes dominate. Additionally, bacterial systems that had immobilized more Fe compared with bacteria-free systems did not immobilize more silica than bacteria-free systems. By comparing molar ratios of (silica in solution)/(bacterially bound Fe), it is evident that insufficient iron is bound to the bacterial surface to act as an effective salt bridge for silica sorption. This appears to be because much of the iron is immobilized by non-bacterially mediated precipitation of phases such as Fe(OH)3 and poorly ordered hydrous iron silicates. It follows that in silica-enriched hot springs, silica and iron immobilization processes are significantly dominated by non-bacterially mediated precipitation. Any bacterially mediated processes are exceedingly small and outside the resolution of these experiments.