Immature organic-rich siliceous chalk (‘oil shale’) and organic-poor limestones of the Maastrichtian-Paleocene Muwaqqar Chalk Marl Formation (MCM) (central Jordan) deposited on the southern Neo-Tethys epicontinental shelf provide a perfect example of carbonate sedimentation in a bioproductive upwelling environment. The MCM sediments have been studied by XRD, SEM, EMPA, sequential extraction, ICP-MS, GC–MS, and FTIR to gain insights into causes of their unusual composition. The sediments are remarkable by exceptionally high enrichment in phosphorus and redox sensitive elements (RSE), mainly Cd (up to 225 ppm), Zn (1500 ppm), and Mo (up to 180 ppm), as well as in Ni, V, Cr, and U, with a total RSE budget reaching 3200 ppm, coupled with up to 23 wt% organic matter and 4.3 wt% sulphur. The bulk organic matter consists of type I/II kerogens sulphurised during sulphate reduction. Redox sensitive metals were brought to sediments mainly by biogenic shuttle, while the terrestrial input was minor, and hydrothermal fluids apparently did not contribute to total RSE. The metals can reside in sulphide (Zn-Cd-(Cu)) in sphalerite or/and würtzite; Fe-Ni-V-Cu-(Mo) in pyrite, carbonate (Zn-Cd-(Mo-Ni-V)), and organic (Ni-V-Cu) phases. Authigenic Cd-rich sphalerite and würtzite are much more abundant than pyrite in immature ‘oil shales’, for three main reasons: (i) S-bearing ligands coordinating Cd and Zn in primary organic matter; (ii) high sulphur in organic matter; and (iii) low concentrations of reactive iron in bottom sediments. Limestones redeposited under oxic environments lose all sulphides, but high Zn (up to 337 ppm) and Cd (up to 29 ppm) become redistributed into the newly formed carbonates. Thus, shelf carbonates of different ages deposited under anoxic/sulfidic conditions in zones of high bioproductivity, as well as their derivative limestones and dolomites, can be the primary Zn and Cd storage for Mississippi Valley-type deposits with high Zn/Pb and Cd/Zn ratios.