Thin-section investigation (polarized-light, cathodoluminescence, and ultraviolet microscopy) combined with isotopic (δ18O, δ13C,87Sr/86Sr) analyses of bulk carbonate samples form the basis for evaluating the diagenetic alteration of Albian–Cenomanian and Maastrichtian density-flow deposits off two segments of the Apulia Carbonate Platform in the Gargano Promontory, Italy. We propose that differential platform uplift south and north of the Mattinata Fault controlled the diagenesis of density-flow deposits during Albian–Cenomanian times. In both cases, the: i) abundant blocky cement and vuggy pores in clasts, and ii) remnant blocky cement on allochems in the corresponding matrix samples with interparticle pores, indicate disintegration of at least partially cemented deposits before failure and reworking into density flows. The abundant rudist fragments suggest that they were sourced from the margin and upper slope. However, the δ13C compositions of the density-flow deposits south and north of the Mattinata Fault are different, and geochemical modeling based on presumed marine and terrestrial δ13C compositions indicates: A) The marine δ13C values of deposits south of the Mattinata Fault suggest that the margin- and upper-slope deposits were subjected to predominantly marine-burial diagenesis before failure. Albian–Cenomanian Sr-isotope ages support the marine-burial diagenetic scenario where strontium was redistributed locally during calcitization of aragonitic allochems and during precipitation of calcite cements. However, post-uplift precipitation of vadose cement in pores formed during marine-burial diagenesis has lowered the δ13C and increased the 87Sr/86Sr ratio in many of the samples. B) Twenty-five km north of the Mattinata Fault, the negative δ13C values suggest that oxidation of terrestrial plants supplied 12C-enriched CO2 to the pore-water carbon pool during subaerial exposures, thus lowering the δ13C compositions of the margin- and upper-slope deposits from values obtained during marine-burial diagenesis. This diagenetic model requires that residual aragonitic and high-Mg calcitic allochems were available in the deposits during penetration of meteoric water. However, the Albian–Cenomanian Sr-isotope ages and the geochemical modeling support a predominantly marine-burial scenario, with intraformational redistribution of strontium during meteoric diagenesis. A similar diagenetic model is envisaged for the Maastrichtian density-flow deposits south of the Mattinata Fault, but the less negative δ13C and geochemical modeling suggest less influence of meteoric diagenesis before reworking. The majority of separate- and touching-vug pores likely also formed during marine burial before failure and reworking of the margin- and upper-slope deposits. The large range in porosity (4–31%) of density-flow deposits with predominantly interparticle pores are inferred to reflect varying degrees of compaction caused by variable overburden thickness as well as sedimentary processes. The results of the present study indicate that the geochemical imprint of meteoric diagenesis can be expected to vary in density-flows deposited along coeval segments of carbonate platforms in tectonically active regions.