Discovery of lacustrine microbialite reservoirs in South Atlantic pre-salt has motivated the search for analogs for perspectives on their deposition and initial porosity. Although previous efforts mapped spatial patterns and produced facies models of large microbial lacustrine systems, details of the origins of microbialite fabrics are less well constrained. To address these unknowns, this study evaluates the influence of organic-matter source, abundance, and growth habit on Holocene microbialite fabrics. Integrated multi-scale analyses characterize fabrics of Holocene microbialites in a small (< 1 km2), shallow (< 1 m), hypersaline, alkaline lake on Crooked–Acklins Platform in the southern Bahamas. The results of analyses indicate systematic distribution of surface sediment across the lake, from various types of unlithified microbial mats to calcareous microbialites; bottom type relates to water depth. Spherules with laminae of radial aragonite are common in organic-rich mats, and can have competitive growth boundaries. Calcareous microbialites in the lake center can reach up to 60 cm tall and 2+ m across, and include macrofabrics and microfabrics that vary considerably, across micrometer to meter scales. Porosity varies from 43 to 59%, in pore types ranging from intra-fibrous (IF), breccia (BR), vuggy (VUG), intra- (WL) and inter-laminar (IL), digitate (DG), to branching (BRA). Microfabrics are not unique to individual macrofabrics, and organic-matter source is similar among fabrics. The abundance of organic matter and growth habit of organics on the outer parts of microbialites varies markedly among fabrics, suggesting that these parameters may control rock fabric. The occurrence of Mg silicates in association with these microbialites may favor preservation of the depositional pores. Although ultimate preservation is unknown, understanding the genesis of primary fabrics may provide insights into possible pore evolution in reservoir analogs.