Chemical mobility of crystalline and amorphous SiO2 plays a fundamental role in several geochemical and biological processes, with silicate minerals being the most abundant components of the Earth's crust. Although the oldest evidences of life on Earth are fossilized in microcrystalline silica deposits, little is known about the functional role that bacteria can exert on silica mobility at non-thermal and neutral pH conditions. Here, a microbial influence on silica mobilization event occurring in the Earth's largest orthoquartzite cave is described. Transition from the pristine orthoquartzite to amorphous silica opaline precipitates in the form of stromatolite-like structures is documented through mineralogical, microscopic and geochemical analyses showing an increase of metals and other bioessential elements accompanied by permineralized bacterial cells and ultrastructures. Illumina sequencing of the 16S rRNA gene describes the bacterial diversity characterizing the consecutive amorphization steps to provide clues on the biogeochemical factors playing a role in the silica solubilization and precipitation processes. These results show that both quartz weathering and silica mobility are affected by chemotrophic bacterial communities, providing insights for the understanding of the silica cycle in the subsurface.