Microbialites form the earliest macroscopic evidence of life, and have always been important in particular aquatic ecosystems. They demonstrate the remarkable ability of microorganisms to provide the foundation for structures that can rival coral reefs in size. Microbialites are generally assumed to form by microbial trapping and binding of detrital grains, by carbonate organomineralization of microbial biofi lms, or by inorganic mineralization around microbial templates. Here we present a signifi cant discovery that modern thrombolitic microbialites in Lake Clifton, Western Australia, gain their initial structural rigidity from biofi lm mineralization by the trioctahedral smectite mineral stevensite. This nucleates in and around microbial fi lament walls when biological processes suppress carbon and Ca activities, leaving Mg to bind with silica and form a microporous framework that replaces and infi lls the fi lament web. After microbial materials are entombed, local carbon and Ca activities rise suffi ciently for aragonite microcrystals to grow within the stevensite matrix and perhaps replace it entirely, with eradication of biogenic textural features. This may explain why many ancient microbialite carbonates lack clear evidence for biogenicity. Stevensite may provide the missing link between microbial organomineralization and subsequent abiotic calcifi cation.