Limestone beds formed in nearly carbonate-free shallow-water mudstones by discontinuous sedimentation and erosion are called hiatus beds. Anaerobic oxidation of organic matter by microbes provided excess alkalinity, inducing carbonate precipitation. A multiphase history of such beds is documented from the Swiss Jurassic by several cementation and dissolution phases. Four cement types occur: micrite as earliest cement (δ13C −10 to −20‰), stellate calcite between micrite-cemented parts (δ13C −5 to −10‰), fibrous calcite cement in dissolution cavities (δ13C < −30‰), and blocky calcite in remaining pores (δ13C −5‰). Except for the late blocky cement, all cements contain pyrite, indicating carbonate precipitation within the sulfate reduction zone. After early cementation by micrite, the beds moved relatively upwards into a shallower geochemical zone and some even to the seafloor because of erosion. Cavities formed during reburial by dissolution in the upper part of the sulfate reduction zone and in the upper part of the methanogenic zone. Strongly reduced sedimentation rates provided the requisite stable geochemical conditions for at least several thousands of years, which permitted precipitation and dissolution of carbonate by biochemical processes and diffusion. This happened on short-lived swells caused by differential subsidence and rotation along listric faults when basement structures became reactivated during the extensional stress regime from opening of the Tethys. During the Jurassic and Cretaceous breakup of Pangea the shelf area increased, and differential subsidence on these newly formed shelves was the main factor responsible for the observed post-Paleozoic maximum in hiatus beds and hiatus concretions.