The giant Pre-salt reservoirs represent most of the oil production in Brazil. The main Aptian sag reservoirs were deposited in a unique and highly complex hyper-alkaline lacustrine setting. These deposits are essentially constituted by fascicular and spherulitic calcite precipitated in a magnesian clay matrix (stevensite, kerolite, and saponite/hectorite). Although vital for understanding the origin and main reservoir quality control, the genesis and interactions of clays and carbonates are still poorly constrained. The detailed petrographic description was focused on 812 thin sections from five wells drilled in the Santos Basin Aptian Barra Velha Formation, combined with cathodoluminescence, UV epifluorescence, and X-ray diffraction analyses. The main syngenetic processes were the deposition of finely laminated peloidal and ooidal Mg-clays, the formation of fascicular calcite crusts on the sediment–water interface, and the redeposition of these materials as intraclasts. Abundant clay peloids engulfed in syngenetic shrubs indicate that calcite and clay precipitation was concomitant, though with highly variable rates. Eodiagenetic phases include matrix-replacive and -displacive spherulites and fascicular shrubs; matrix-replacive blocky calcite and dolomite; lamellar carbonates filling matrix shrinkage pores; and microcrystalline calcite, dolomite, and silica replacing the Mg-clay matrix. The preferential dolomitization and calcitization of peloidal layers were most likely due to their higher permeability and larger specific surface. Matrix-replacive saddle dolomite, macrocrystalline calcite, and dawsonite are interpreted as mesodiagenetic or hydrothermal phases after significant matrix dissolution. Unraveling the processes of the formation and alteration of the carbonates and clays and their interactions in the Pre-salt deposits is essential for constraining the depositional and diagenetic conditions in their unique environments and their diagenetic overprinting and for decreasing the exploration risks and increasing the production of those extraordinary reservoirs.