ABSTRACT Silicified peritidal carbonates of the Tonian Draken Formation, Spitsbergen, contain highly diverse and well‐preserved microfossil assemblages dominated by filamentous microbial mats, but also including diverse benthic and/or allochthonous (possibly planktonic) microorganisms. Here, we characterize eight morphospecies in focused ion beam (FIB) ultrathin sections using transmission electron microscopy (TEM) and X‐ray absorption near‐edge structure (XANES) spectromicroscopy. Raman and XANES spectroscopies show the highly aromatic molecular structure of preserved organic matter. Despite this apparently poor molecular preservation, nano‐quartz crystallization allowed for the preservation of various ultrastructures distinguished in TEM. In some filamentous microfossils ( Siphonophycus ) as well as in all cyanobacterial coccoids, extracellular polysaccharide sheaths appear as bands of dispersed organic nanoparticles. Synodophycus microfossils, made up of pluricellular colonies of coccoids, contain organic walls similar to the F‐layers of pleurocapsalean cyanobacteria. In some fossils, internal content occurs as particulate organic matter, forming dense networks throughout ghosts of the intracellular space (e.g., in Salome svalbardensis filaments), or scarce granules (in some Chroococcales ). In some chroococcalean microfossils ( Gloeodiniopsis mikros , and also possibly Polybessurus ), we find layered internal contents that are more continuous than nanoparticulate bands defining the sheaths, and with a shape that can be contracted, folded, or invaginated. We interpret these internal layers as the remains of cell envelope substructures and/or photosynthetic membranes thickened by additional cellular material. Some Myxococccoides show a thick (up to ~ 0.9 μm) wall ultrastructure displaying organic pillars that is best reconciled with a eukaryotic affinity. Finally, a large spheroid with ruptured wall, of uncertain affinity, displays a bi‐layered envelope. Altogether, our nanoscale investigations provide unprecedented insights into the taphonomy and taxonomy of this well‐preserved assemblage, which can help to assess the nature of organic microstructures in older rocks.