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Outcrops of the Middle Eocene in northern Egypt represent a Tethyan reef-rimmed carbonate platform with bedded inner-platform facies. The diagenesis of these outcrops was studied in detail. The facies are characterized by a reef core, back reef and outer lagoon, shoal, inner lagoon, and tidal flat carbonate sequences. The diagenetic sequences on the scleractinian corals and foraminifers were thoroughly examined. These sequences show various diagenetic features during episodes of fluctuating sea levels and appear to be related to the primary composition of the studied components and the transgressive-regressive cycles. The carbonate diagenetic history of the examined samples successively includes marine-phreatic, mixed marine-meteoric, and shallow burial diagenesis. Most of the coral samples are affected by micritization and neomorphism and most of the foraminiferal samples are affected by micritization, dolomitization, glauconitization, or cementation. A sequence-stratigraphic analysis was carried out by integrating field and laboratory studies. The investigated sections were subdivided into three third-order sequences named S1, S2, and S3. The distribution of diagenetic fabrics was compared to a sequence stratigraphic framework. This has resulted in, for example, recording isopachous cement and autochthonous glauconitization mostly in the transgressive parts, while dolomitization, drusy cement, and biomoldic and vuggy porosities are recorded in the regressive parts; dedolomitization, allochthonous glauconitization, and ferrugination processes occurred at the sequence boundaries.