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 biofilms, or by inorganic mineralization around microbial templates. Here we present a significant discovery that modern thrombolitic microbialites in Lake Clifton, Western Australia, gain their initial structural rigidity from biofilm mineralization by the trioctahedral smectite mineral stevensite. This nucleates in and around microbial filament walls when biological processes suppress carbon and Ca activities, leaving Mg to bind with silica and form a microporous framework that replaces and infills the filament web. After microbial materials are entombed, local carbon and Ca activities rise sufficiently 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 calcification.