Laminated accretionary carbonate structures known as stromatolites are a prominent feature of the sedimentary record over the past 3,500Myr (ref. 1). The macroscopic similarity to modern microbial structures has led to the inference that these structures represent evidence of ancient life. However, as Archaean stromatolites only rarely contain microfossils, the possibility of abiogenic origins has been raised. Here, we present the results of nanoscale studies of the 2,724-Myr-old stromatolites from the Tumbiana Formation (Fortescue Group, Australia) showing organic globule clusters within the thin layers of the stromatolites. Aragonite nanocrystals are also closely associated with the organic globules, a combination that is remarkably similar to the organo-mineral building blocks of modern stromatolites. Our results support microbial mediation for the formation of the Tumbiana stromatolites, and extend the geologic record of primary aragonite by more than 2,300Myr (ref. 6).