The Upper Muschelkalk sedimentary record constitutes a major transgressive pulse of north-eastern Iberia during the Ladinian. This record is arranged in two transgressive–regressive (T–R) sequences formed by two stepped microbial-dominated carbonate ramp systems where accommodation was mainly controlled by extensional faults. This study seeks to gain new insights into how the evolution of syn-rift subsidence controls the creation of accommodation space, the depositional styles and, especially, the palaeogeographical domains where specific microbialites developed (thrombolites and stromatolites). Thrombolite bodies (at least 40 m thick) display two types of architecture, biostromal and mud-mounded and stromatolite bodies (at least 7 m thick) consist of tabular and domed, head-shaped morphologies. Domed and mounded forms are usually developed during stages of increasing accommodation rates, low-to flat-nelief forms tend to grow in association with periods of low accommodation rates. A sea-level fall of at least 50 m occurred at the end of the Early Ladinian leaving the platform subaerially exposed. As a result, a prominent karst with significant erosional incisions and profuse collapse breccia fillings was formed in the inner and middle ramp settings. The resultant subaerial unconformity bounds T–R sequences 1 and 2. Subsidence curves display two stages of rapid/decelerated total subsidence, constituting two discrete rift/post-rift pulses in the large Triassic rifting period: (i) Buntsandstein – Middle Muschelkalk, and (ii) Late Muschelkalk – Imon Formation (Rhaetian). The second pulse is characterized by a rapid syn-rift subsidence during the Late Muschelkalk, and a decelerated post-rift subsidence throughout the deposition of Keuper facies and Imon Formation. The Late Muschelkalk rapid syn-rift pulse of total subsidence produces gains in accommodation, which controls the development of the stromatolites and thrombolites (biostromes and mud-mounds).