The diagenesis in the organic-rich Cretaceous to Eocene Al Hisa Phosphorite Formation (AHP), Muwaqqar Chalk Marl Formation (MCM) and Umm Rijam Chert-Limestone Formation (URC) formations of Jordan can be linked directly to the fluctuating sedimentary environment of this shelf depositional system in the Middle to Late Eocene, and its influence on the composition of the deposited sediment and the early burial diagenetic environment. Most cementation was early, mostly within the first 10 m of burial, perhaps entirely within the first 100 m of burial. We propose that the siliceous cements are derived from biogenic silica, probably of diatoms, deposited in a shelf of enhanced productivity. Volumetrically, the most important processes were the redistribution of biogenic opal-A (diatoms) and calcite to form pervasive, layered and nodular cements. The formation of the silica and carbonate cements is closely linked through the effects their dissolution and precipitation have on pore fluid chemistry and pH. The chert beds have a biogenic silica origin, formed through replacement of diatoms and radiolaria by opal-CT, and subsequently by quartz. Calcite cement has carbonate derived from microbial diagenesis of organic matter and calcium derived from seawater. The Mg for early dolomite may have been generated by replacement of opal-CT by quartz, ore dissolution of unstable high Mg calcite bioclasts. The silica and carbonate diagenetic processes are both linked to microbial diagenesis of organic matter, and are intimately linked in both time and space, with pH possibly influencing whether a silica or a carbonate mineral precipitates. The paucity of metal cations capable of precipitating as sulphides is crucial to the creation of acidic pore water favourable to silica precipitation, either as opal-CT, chalcedony or quartz. The lack of clay minerals as a sink for the Mg required for opal-CT polymerisation is the principal factor responsible for the remarkably early silica cementation. All the diagenetic processes, with the probable exception of the opal-CT to quartz transition are early, almost certainly within the first 10 m of burial, possibly much less. A paragenetic sequence is presented here based on these two cores that should be tested against a wider core distribution to see whether this diagenetic history can be generalised throughout the basin. Warm bottom water temperatures probably led to silica diagenesis at much shallower burial depths than occurs in many other sedimentary basins. Silicified layers, in turn, commonly host fractures, suggesting that mechanical properties of the strata began to differentiate at a very early stage in the burial cycle. This has wide implications for processes linking diagenesis to deformation.