Detailed petrographic and geochemical studies of pore-filling cements and replaced (epigenic) membranes of some organic-walled microorganisms preserved in the Neoproterozoic Doushantuo Lagerstätte (China) are based on an energy dispersive system (EDS) of elemental mapping attached to backscattered MEB. Their microcrystalline apatite (collophane) occurs predominantly as phosphatized microbial pseudomorphs: phosphatic crusts of chasmolithic bio-films (or microstromatolites) and globular clusters occur lining intraparticular porosities. Three major pre-compactional cement types are identified on algal thalli, embryos and vase-shaped microfossils: epigenic collophane (by replacement of membranes), polyphasic filling of collophane and crystalline apatite and fluorapatite within intraparticular porosities (some of them microbially mediated), and latest carbonate precipitation filling the remaining intraparticular porosities (preserved at present as dedolomitized calcite). P2O5 concentration has a clear peak in the microbial pseudomorphs and uniformly low concentrations elsewhere, whereas MgO, Na2O, K2O and SiO2 show a slight increase in concentration through successive cements. These geochemical trends evidence a slight change of pore fluids accompanied by a final rise in pH, presumably following the main interval of decay, which favoured precipitation of CaCO3 postdating that of apatite.