Hydrothermal diagenesis during the Zagros Orogeny produced three phases of saddle dolomites (SD1, SD2, and SD3) and two phases of blocky calcites (CI and CII) in the studied sections of Bekhme Formation (Fm) (Campanian–Maastrichtian). Field observations, as well as petrographic, cathodoluminescence (CL), Scanning Elecron Microscope (SEM), and oxygen–carbon isotope analyses, indicated that the unit went through multiple submergence–emergence phases after or during hydrothermal diagenesis. These phases resulted in a characteristic calcretized 2–6-m-thick layer within the Bekhme Fm. Several pedogenic textures (e.g., alveolar, pisolite, and laminar fabric microfeatures) were observed. Strong evidence of microbial alteration and diagenesis in this formation brings new insights into its depositional history. The microbial activities developed on the original mineral surface were associated with a great variety of processes including dissolution, re-precipitation, replacement, open-space fillings, microporosity development, grain bridging, and micritization. Probable oxalate pseudomorphs embedded in these fabrics and regular filaments preserved along crystal boundaries suggest the activity of fungi, while frequent coccoidal, rod-like, and chain-like forms attached to the surfaces of dolomitic and calcitic crystals point to bacterial colonization. Extracellular polymeric substance (EPS) was often visible with fungal and bacterial forms. These features, together with stable isotope data, invoke that near-surface conditions occurred sporadically in the Bekhme Fm after the first generation of hydrothermal dolomitization. These new findings allow recognition of unreported sedimentological phases based on new evidence in the Spelek–Sulauk area during the Upper Cretaceous.