Abstract Organism-environment feedbacks in Precambrian platformal carbonates and reefs were strongly influenced by the activities of diverse microbial ecosystems. Microfacies studies of representative platformal microbial carbonates, comprising cyanobacterial mat, stromatolites and giant ooids, from the Late Archaean Ghaap Group of South Africa have provided compelling evidence for an intimate relationship between taphonomic evolution, fabric development and mineralogy in rocks of the Gamohaan and Boomplaas formations. Cements, both in fold hinges and between the limbs of slump-folded and contorted, partially-degraded, pyritiferous stromatolitic laminae, were precipitated after deformation of organic fabrics, but before or during their compaction, indicating that cementation took place at the same time as anoxic organic degradation involving bacterial sulphate reduction. Bundles and strands of the organic remains of filamentous cyanobacteria, in varying states of degradation in both stromatolites and ooids, have been preserved by mineralization. Structural detail is usually best preserved in calcite, where cyanobacterial sheaths, 10 μm to 25 μm in diameter and hundreds of micrometres in length, can be clearly seen. Petrographic analysis of the microfabrics using cathodoluminescence reveals dolomicrite nucleated along the outer margin of some sheaths. Dolomicrospar and dolospar fabrics developed progressively in association with increasing sheath degradation, as evidenced by the sequential loss of structural detail, culminating in a xenotopic fabric comprising brown, inclusion-rich, anhedral crystals with irregular boundaries. Biogeochemical modelling supports a genetic link between bacterial sulphate reduction and (1) calcite precipitation in the contorted laminae, and (2) replacive dolomitization of the calcific matrix in the stromatolites and ooids. The evidence indicates that anoxic organic diagenesis was an essential and major process in controlling carbonate precipitation and mineralogy in widespread microbialitic sediments of the Ghaap Group, a depositional environment analogous to many other Archaean, Proterozoic and, during periods of biotic stress, some Phanerozoic carbonate platforms.