Among the most important traces of the microbial ecosystems that colonized the Archean Earth (2.5 to 4 billion years) are some carbonate deposits of peculiar morphologies called stromatolites. Although we know that such deposits form under the influence of microbial mats in modern environments, the origin of Archean “fossil” stromatolites is still debated. The use of microscopy and spectroscopy allowed us to study the organic matter and associated minerals within the rock down to the nanoscale. This study revealed the presence of cell-like organic globules within the Tumbiana stromatolites (2.7 billion years old). These globules are intimately associated with nanocrystalline aragonite. The similarity of this association with the organo-mineral nano-composites forming modern stromatolites argues in favor of the biogenicity of the Tumbiana stromatolites. The finding of such presumably unstable aragonite extends the geological record of this mineral by 2.3 billion years. The systematic study of the organo-mineral associations throughout these stromatolites shows the absence of textures characteristic of organic matter remobilization in association with the globules, hence supporting their interpretation as microfossils. This distribution as well NEXAFS and EDX spectroscopy of the organic matter suggests that the globules were preserved owing to a concurrent action of organic matter sulphurization and encapsulation by minerals.