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Microbialites are formed through two processes, the trapping and binding of sediment grains and mineral precipitation. Sediment trapping and binding result in coarse sandy textures, whereas fine micritic textures are produced by mineral precipitation. Although well-studied modern microbialites (e.g. Bahamas and Shark Bay) are formed through the former process, purely trapped-and-bound examples are rare throughout the geologic record and limited to shallow-marine environments. Through the use of conventional microscopy and 3D micro-computed tomography (µ-CT) scanning, this study found that South African coastal microbialites have a primarily mineral precipitated texture, although detrital material is included sporadically. Furthermore, these modern microbialites exhibit both micritic and fibrous layering with high porosity. The novel use of 3D microtomography rotational scans has revealed that microbialites are extensively burrowed by metazoan activity and was also able to distinguish the occurrence and distribution of heavy minerals and detrital shell material in the samples. Some of the detrital grains appeared to be accidental/random inclusions, while in other cases the metazoan burrows provided space for the accumulation of sediment once abandoned. In both cases, sediment was incorporated as a product of intermittent accumulation, rather than systematic trapping and binding. The microfabric texture of South African microbialites is therefore a function of both biological (e.g. microbially mediated precipitation) and environmental (e.g. sporadic sediment deposition and inorganic cementation) influence. Overall, the findings presented here highlight the importance of these systems regarding microbialite formation, ichnology and taphonomy., (© 2021 John Wiley & Sons Ltd.)