Early-diagenetic cementation of tropical carbonates results from the combination of numerous physico-chemical and biological processes. In the marine phreatic environment it represents an essential mechanism for the development and stabilization of carbonate platforms. However, diagenetic cements that developed early in the marine phreatic environment are likely to become obliterated during later stages of meteoric or burial diagenesis. When rock samples are studied, this complicates the recognition of processes involved in cementation, and their geological implications. In this contribution, a petrographic microfacies analysis of Holocene Halimeda segments collected on a coral island in the Spermonde Archipelago, Indonesia, is presented. Through electron microscopical analyses of polished sections, this study shows that segments are characterized by intragranular cementation of fibrous aragonite, equant Mg calcite (3.9 – 7.2 Mol% Mg), bladed low Mg calcite (0.4 – 1.0 Mol%) and mini-micritic Mg calcite (3.2 – 3.3 Mol% Mg). The co-existence and consecutive development of fibrous aragonite and equant Mg calcite results initially from the flow of oversaturated seawater above the aragonite template, followed by an adjustment of cement mineralogy towards Mg calcite due to reduced permeability and fluid flow rates in the pores. Growth of bladed low Mg calcite cements on top of etched substrates of equant Mg calcite is explained by shifts in pore water pH and alkalinity through microbial sulfate reduction. Microbial activity appears to be the main trigger for the precipitation of mini-micritic Mg calcite as well, based on the presumable detection of an extracellular polymeric matrix during an early stage of mini-micrite cement precipitation.