Early Jurassic shallow water carbonate environments of Tethys experienced important changes in a context of rifting that climaxed with the final break-up of Pangea. This time was also characterized by major perturbations of the global carbon cycle, some of which likely linked to the emplacement of large igneous provinces. At the Sinemurian–Pliensbachian (Early Jurassic) transition a globally recognized carbon isotope perturbation named “S–P Event” was found. In the western Tethys, this coincided with important architectural changes in the carbonate platforms which switched from peritidal flats to subtidal rimmed lagoons. A similar evolution in carbonate systems was observed during the Carnian Pluvial Episode (Late Triassic) when a global carbon isotope perturbation coincided with the demise of microbial carbonate platforms in the Tethys. In this paper, new carbonate and organic carbon isotope records and quantitative petrography data (modal analysis) from the deep- and shallow-water Sinemurian–Pliensbachian sedimentary successions exposed in the central Southern Alps of Italy are presented. Data show that across two negative carbon isotope excursions the carbonate factory abruptly changed and a drop in the microbial fraction of the carbonate occurred. This suggests that environmental modifications associated with these isotope excursions impacted the type of carbonate production and were a key-factor in determining the evolution of Tethyan carbonate platforms. New results and a comparison between the S–P Event and the Carnian Pluvial Episode highlight striking commonalities and imply that the demise of microbial carbonate systems coincident to isotope perturbations is not an isolated event in geologic history. Microbialites, therefore, do not necessarily represent “crisis facies” following extinction events. Rather, their development or demise appears linked to yet poorly understood mechanisms governing the interaction between global climate changes and shallow-water carbonate sedimentation.