After the first great oxygenation event (GOE), microorganism communities flourished in various habitats in shallow marine settings as a response to elevated oxygen contents in atmosphere and seawater. Abundant microorganisms have been reported from microbialites and siliceous dolomites and siliciclastic rocks. Here we report a diverse microfossil assemblage from siliceous granules within chert grainstones of the ca. 1.6 Ga late Paleoproterozoic Dahongyu Formation in the Jixian section, North China. These microfossils are confined to granules and absent in inter-granular chalcedony interpreted as cementing matrix. The microfossil assemblage is made up of the five morphotypes: two types of large spheroidal forms, much smaller unicells, unbranched filaments of cyanobacterial affinity, and chain-like filaments (CLFs) composed of hematitic pseudomorphs after pyritization. The CLF possesses a carbonaceous sheath structure which is mostly obscured by previous pyrite crystals, suggesting a potential bacterial origin. The unique morphology and distinctive chemical composition both distinguish these filamentous objects from filaments known in the Archean and Proterozoic worldwide. However, similar CLFs have been found in a variety of lithofacies worldwide, and coexist with other microfossils or microbial mats, implying that they all may represent a once-widespread group of microbes. The hosting granules are interpreted as depositional products that were transported from shallow marine into a deeper ramp setting, and the microfossils and mat debris therefore likely represent a phototrophic community. The inferred high minus-cement porosity and the predominantly grain-supporting texture of these granules signal the early silicification and cementation. Thus, chert grainstones formed in this way may effectively preserve traces of early life and provide snapshots of early microorganisms after the GOE.