This work studies the mineralogical and geochemical features of ooidal ironstone formation of the Upper Cretaceous Ayat Formation located in the Turgay depression (Kazakhstan). The origin of ooidal ironstone deposits has been the subject of many discussions for a long time. These results present diagenetic conditions of the marine ironstone precipitation in the Ayat Formation. Various authigenic minerals, such as siderite, glauconite, goethite, pyrite, hydroxylapatite, wurtzite, and barite indicate fluctuations in the different geochemical conditions during the diagenesis of marine sediments of the Ayat Formation. The precipitation of in situ pyrite and wurtzite was controlled by an oxygen-deficient environment at the interface between water and sediment, which was accompanied by bacterial sulphate reduction under seabed conditions and, in consequence, by the concentration of sulfides. The authigenic assemblage of siderite, wurtzite, and barite indicates an integrated process of their input to site the sedimentation. The stable isotopic composition of siderite supports the microbial carbonate origin by decomposing the organic matter. However, geochemical features (the pattern Co/Zn vs (Co + Ni + Cu)) evidence the hydrogenous precipitation of iron. It involves the interaction of two central in situ processes to form Ayat ooidal ironstones. One of them is the iron precipitation from the bottom water, and the second is the microbial generation of hydrocarbons. Marine Ayat and channel Lisakovsk ironstones have similar features of bulk rock geochemistry. It reflects the exact environments of the ooidal iron ore formation, while the wall rocks have distinctive facies conditions.