The depositional age and diagenetic history of the Upper Barra Velha carbonates are poorly understood. To clarify the geochronology of these events and the behavior of the U-Pb isotopic system in carbonates, we conducted an integrated petrographic, QEMSCAN imaging, and in situ U-Pb dating study of calcites and dolomites from the Barra Velha Formation, in the central Santos Basin (SE Brazil). Our results span three geochronological intervals, which are ∼125 Ma, ∼116-114 Ma, and ∼105-100 Ma. The U-Pb isotopic system of calcite allochems was disturbed, yielding ages of ∼115 Ma and ∼105-100 Ma. These ages coincide with magmatic and hydrothermal events in the pre-salt. Dolomites showed that geochronological disturbance of carbonate components may not be pervasive but rather related to fluid-rock interactions and properties of rocks and their constituents such as mineralogy, porosity and permeability. This is evidenced by the U-Pb system of non-porous, non-permeable, and less reactive dolomitic aggregates remaining undisturbed. Eodiagenetic microcrystalline and fine dolomite rhombs provided evidence of Barremian ages, challenging the belief that the Upper Barra Velha deposits are Aptian. Other eodiagenetic dolomites occur as ∼117 Ma eodiagenetic lamellar dolomites, as pseudomorphic dolomites that underwent U-Pb alteration at ∼100 Ma, and as ∼112 Ma pervasive rhombohedral dolomites associated with Mg-rich fluids percolation in the Upper Barra Velha carbonates. Blocky dolomite and saddle dolomite cements have ages of ∼100 Ma, with saddle dolomite constraining the latest silicification event as > 100 Ma. This research elucidates significant geological events, processes, and factors (including magmatic activity, hydrothermal alteration, fluid-rock interactions, and petrographic and mineralogical controls) that influenced the ages of the Upper Barra Velha carbonates. Moreover, it aids in reconstructing the depositional and diagenetic history of the Barra Velha Formation and enhances the understanding of the Santos Basin tectonothermal evolution.