The Miocene dolomite-chert microbialites studied here offer a complete record of the geochemical cycles of silicate weathering and the subsequent formation of secondary products. The microbialites were formed in lacustrine systems during the Miocene of the Duero Basin, central Spain. Mineralogical, chemical and petrographic results provide evidence of the mediation of microbes in early weathering and by-product formation processes. Irrespective of the composition, the surfaces of the grains were subject to microbial attachment and concomitant weathering. Palaeo-weathering textures range from surface etching and pitting to extensive physical disaggregation of the minerals. Extreme silicate weathering led to the complete destruction of the silicate grains, whose prior existence is inferred from pseudomorphs exhibiting colonial textures like those recognized in the embedding matrix. Detailed petrographic and microanalytical examinations of the weathering effects in K-feldspars show that various secondary products with diverse crystallinity and chemical composition can coexist in the interior of a mineral. The coexistence of by-products is indicative of different microenvironmental conditions, likely created by microbial reactions. Thus, the presence of varied secondary products can be used as a criterion of biogenicity. Intensive alteration of P-bearing feldspars suggests that mineral weathering may have been driven by the nutrient requirements of the microbial consortium involved in the precipitation of dolomite. The rock record provides useful information on mineral weathering mediated by microbes.