The thickness of microbialite crusts in Holocene barrier and fringing reefs of Bora Bora was quantified in drill cores from windward and leeward settings to decipher possible spatial and temporal patterns as well as controlling environmental factors. Based on the analysis of 145 occurrences in nine rotary cores, microbialite thickness ranges from 0.1–11.0 cm with an average value of 1.97 cm (SD = 2.47). Microbialites occur only from 9.5–5.6 ka corresponding to a period of rapid sea-level rise and reef accretion in the early Holocene. However, there is no statistically significant correlation between microbialite thickness and reef accretion rate. Also, there is no correlation between microbialite abundance and age. The upcore increase in microbialite abundance, however, suggests that time available for carbonate accretion in shallow water plays a role in microbialite formation. Crust thickness is greater on windward as compared to leeward fringing reef settings indicating that flushing of pore space is a likely factor controlling microbialite accretion. Other environmental factors potentially being responsible for the Holocene decrease in microbialite abundance include climate, i.e., decreasing temperatures and precipitation (supporting nutrient input by runoff) as well as decreasing seawater alkalinity. At the mesoscale, structureless and laminated microbialites are by far the most common types. Coated debris, boring infill, and digitate types are less common. Textures at the microscale, including laminated, clotted, and peloidal, do not necessarily match mesoscale textures. The Bora Bora microbialites consist in more or less equal parts of high-magnesium calcite and aragonite. The δ13C values range from +3.0 to +4.1‰ and the δ18O from -0.8 to +0.1‰. The contents of easy soluble sulfate (ESS) and carbonate associated sulfate (CAS) are relatively high. The δ18OCAS (+11.0 to +12.7‰) and δ34SCAS values (+21.9 to +23.6‰) exceed the seawater sulfate standard NBS-127 value and are in the same range as observed in other cryptic, Holocene reefal microbialites. The Bora Bora microbialites contain lipid biomarkers derived from sulfate-reducing bacteria (2–8 wt%), marine plankton, land plants, and unspecified bacteria. The former include branched, short-chain fatty acids and terminally branched fatty acids, whereby iso-fatty acids are more abundant than anteiso-fatty acids. Other compounds with terminally branched alkyl chains include iso- and anteiso-C15 and -C17 alcohols, which are interpreted as degradation products of monoalkyl glycerol ethers (MAGE). Collectively, the organic and inorganic geochemical data together with the sedimentological and mineralogical data suggest that sulfate-reducing bacteria were involved in microbialite development. The temporal and spatial distribution patterns suggest that factors such as exposure to waves and currents, time, nutrient availability, alkalinity, and climate play important roles, however, more quantitative data from other occurrences are needed to be able to better discriminate among them.