Carbonate concretions hosted within organic carbon-rich shale sequences represent unique archives of often exceptionally preserved fossil biota. Besides providing high-fidelity preservation, their geochemical signatures can provide insight into the physical and chemical processes during early and later-stage concretion growth. Here, two fossiliferous carbonate concretions of the late Early Cretaceous Santana Formation (Araripe Basin, north-east Brazil) are analysed with an integrative geochemical approach including μ-XRF scanning, δ13C, δ18O, 87Sr/86Sr and Δ47 (clumped isotope thermometry). Individual concretions show a concentric internal zonation with the outermost layer being composed of millimetre thick cone-in-cone calcite. A strong covariance of δ13C and δ18O values of the fine-crystalline concretion body indicates mixing of two different carbonate phases and supports a scenario of temporally separated pervasive growth stages. Microbially-mediated formation of an early porous calcite framework was controlled by the combined processes of fermentation and methanogenesis around the decaying carcass, forming localized environments within a zone of sulphate reduction. Microbial sulphate reduction is indicated by the concentric enrichment of pyrite in the outer part of the concretion body and by high pyrite abundance in the surrounding shale. Information on the later-stage diagenetic processes affecting the Santana concretions can be derived from the outermost fringing cone-in-cone calcite. The carbonate precipitating fluid was characterized by a more or less marine δ18O composition (calculated δ18Oporewater = −1·0 to −1·8‰) and by radiogenic Sr-isotope ratios (up to 0·713331 ± 7·0*10−6), the latter probably reflecting modification due to interaction with the surrounding shale or, alternatively, with underlying evaporitic sulphate deposits influenced by strong continental inflow or with crystalline basement rocks. The Δ47-derived temperature estimates range between 37°C and 42°C ± 5, indicating precipitation of the cone-in-cone calcite at a depth of 650 to 850 m, which is only half as much as the maximum burial depth derived from existing fission-track data. Overall, the study of fossiliferous carbonate concretions in organic carbon-rich sedimentary sequences can reveal a complex growth history spanning incipient microbially-influenced precipitates as well as later-stage burial diagenetic phases.