Three different types of silica, (1) quartz sand, (2) crystalline (scepter) quartz, and (3) commercial glass, subjected to biological growth were investigated for evidence of biologically induced breakdown. The results of laboratory experiments with biofilms on quartz sand and glass were compared with material from the field. Microscopic (optical and SEM) analysis of quartz sand weathered in vitro by a microbial community of cyanobacteria, diatoms and heterotrophic bacteria demonstrate grain diminution of a sand fraction of North Sea sediment. The microbial community changes the minerals in the vicinity of the living cells, which leave their mark on the quartz surface in form of imprints, depressions and pits. Subsequently microbial growth on the surface brought about a general decrease of the grain size in the layer beneath a biofilm. Imprints of diatoms on glass surfaces colonized by diatoms and heterotrophic bacteria confirm the chemical etching activity of these organisms. Mixed cultures of diatoms and bacteria show depressions corresponding to the shape of individual cells. Our experiments confirm that diatoms, heterotrophic bacteria and cyanobacteria from natural biofilms can actively attack quartz and glass. Microscopic analysis of an idiomorphic scepter quartz crystal from a Tepui weathering environment reveals that the associated biofilms can create a local shift in the pH from 3.4 (pH of water on the Tepui) to evidently higher than 9 (necessary for quartz dissolution). The quartz covered with a biofilm is partially perforated to a depth of more than 4 mm. We conclude that biofilm growth in marine (sub-aquatic) and terrestrial (sub-aerial) conditions can significantly increase the breakdown of silica in the amorphous (glass), sub-crystalline (chert), crystalline and granular forms of quartz. Microbial growth may therefore substantially modify the processes of transformation of a major rock forming mineral of great chemical and physical resistance.