The timing and causal relationships between the pronounced negative C isotope excursion and paleoenvironmental perturbations associated with the Toarcian oceanic anoxic event (Early Jurassic) remain unclear, particularly because biotic crises and carbonate production decrease appear to have been initiated earlier than the main C isotope anomaly. Here we present a new quantification of Late Pliensbachian–Early Toarcian calcareous nannofossils abundance and size from the Peniche reference section (Portugal) together with O and C isotope records of well-preserved brachiopod shells from the same section. The brachiopod shell δ13C curve parallels that of bulk carbonate and records two pronounced negative isotopic excursions, close to the Pliensbachian-Toarcian boundary (∼−2‰) and during the Toarcian oceanic anoxic event (∼−3.5‰). Our results indicate that both C isotope negative excursions were characteristic of benthic and shallow-water environments, suggesting that these two carbon cycle perturbations affected all epioceanic reservoirs. Coeval shifts toward lower values of brachiopod oxygen isotope compositions and closely correlated northward migrations of Mediterranean ammonite fauna suggest that both events coincided with major rises in seawater temperatures, probably as a result of increased CO2 levels and enhanced greenhouse conditions. CO2-induced changes in seawater chemistry likely affected the calcification potential of both neritic and pelagic systems, as evidenced by synchronous drops of platform-derived carbonate accumulation and drastic reductions in size (>3 μm) of the main pelagic carbonate producer Schizosphaerella. We suggest that the Early Toarcian paleoenvironmental crisis occurred in two distinct episodes that were most likely related to two successive phases of intense volcanic degassing in the Karoo-Ferrar province.