This study presents a detailed investigation into the microfacies, geochemistry, and depositional environments of carbonate rocks from the southern Benue Trough and eastern Dahomey Basin. This analysis involved a combination of techniques, including X-ray diffraction, X-ray fluorescence, scanning electron microscopy with energy-dispersive X-ray spectroscopy and thin-section petrographic examination. Samples from the Igumale Formation of the southern Benue Trough and samples from Ewekoro Formation of the eastern Dahomey Basin were analyzed, offering insights into their mineral compositions, elemental distributions, and depositional environments. In each basin, two carbonate microfacies were identified. The two microfacies found in the Igumale Formation were recognized as micritic bioclastic packstone and sandy bioclastic wackestone. In the Ewekoro Formation, the two microfacies recognized were bioclastic packstone and sparitic peloidal wackestone. The X-ray diffraction analysis of samples from both basins revealed a dominance of calcite. X-ray fluorescence analysis showcased calcium oxide and calcium as the predominant oxide and elements in both basins with varying concentrations. Scanning electron microscopy-energy-dispersive X-ray spectroscopy results unveiled the elemental composition with calcium and silicon emerging as major constituents. The photomicrographs suggest distinct depositional conditions for both samples with those from the Igumale Formation showing evidence of shallow marine and that of the Ewekoro Formation suggesting calm marine environments comprised of fined grained carbonate rocks containing fossils. This study has provided detailed understanding on the nature, microfacies types, mineralogical composition, depositional environment and diagenetic processes of Cretaceous-Paleocene carbonate rocks within the studied basins. Display omitted •Carbonate microfacies characterization was performed in selected sedimentary basins in Nigeria.•Integration of carbonate microfacies and a sedimentological approach was used to establish paleodepositional conditions.•The use of petrographic study was used to investigate sedimentology, microfacies association and the paleoenvironment of the carbonate facies.•The use of geochemical index was used to reveal the original sources of the carbonate sediments in the basin.•Integration of SEM and XRD data for understanding the carbonate mineral formation processes, crystal growth and its morphology.•Integration of sedimentological, petrological and geochemical data is key in highlighting poor to fair reservoirs, bioclastic packestone to sandy bioclastic wackestone deposited in shallow marine carbonate environment.