Filamentous and coccoidal microfossils have been reported since the 1950's from a range of granular cherts from the late Palaeoproterozoic southwestern Superior Craton, Canada-United States. However, the chemical and mineral compositions of granules, the presence of microfossils in granules, and the common presence of granules in intercolumnar space of stromatolitic chert are poorly documented and explained. Furthermore, the depositional model for the origin of granules in wave-agitated waters does not entirely explain their mineral diversity nor their characteristic morphologies and patterns. We report on the crystallinity of organic matter, mineral diversity, and compositions of microfossils in granules from three different kinds of late Palaeoproterozoic cherts, namely phosphatic, organic, and haematitic. Stromatolitic organic-rich chert from the Gunflint Fm contains granules with euhedral carbonate and equidistant concentric laminations of organic matter, akin to fractal patterns from the Belousov-Zhabotinsky (B-Z) chemically-oscillating reaction. These granules also contain authigenic anatase, ferric-ferrous silicates, and Fe-oxides. Filamentous and coccoidal microfossils similar to those of the Gunflint occur in chert from the Biwabik Formation and share morphology, and co-occur with Mn-siderite and apatite. Granules in phosphatic chert in the Michigamme Formation often contain filamentous and coccoidal microfossils composed of organic matter, sericite, and apatite. Bulk carbonate associated with these Michigamme granular phosphatic chert beds has systematically negative δ13Ccarb values around −3.1±0.9‰ (1σ) and δ18Ocarb-SMOW between +20.8 and +30.7‰, which suggest some contribution from the diagenetic oxidation of organic matter. Notably, residual carboxylic acid is detectable in C-XANES spectra of organic matter from granular phosphatic chert, which is a residual reactant of B-Z type reactions. Along with previously reported observations of pyritised microfossils from the Gunflint Formation, these distinct mineralogies indicate variable modes of preservation for the products of chemically-oscillating reactions that likely relate to the availability of different oxidants in the diagenetic environment. We conclude that the late Palaeoproterozoic shallow-marine environments of the Lake Superior area were populated by morphologically similar micro-organisms, and that the diagenetic oxidation of organic matter through chemically-oscillating reactions contributed to the formation of spheroidal rosettes, granules, and concretions during a late Palaeoproterozoic Great Putrefaction Event. Granules in chert that contain organic matter or microfossils thus provide a reliable petrographic context to search for a record of putrefaction of microbial life on the early Earth and on other ancient planetary surfaces.