In the aftermath of the Permian-Triassic boundary mass extinction (~252 Ma) ― the most dramatic biotic crisis of the Phanerozoic ― changes in climate, the carbon cycle, and biodiversity patterns remained extremely variable for several million years. In particular, the Smithian-Spathian boundary crisis, which occurred ca. 1.5 Ma after the Permian-Triassic boundary, coincided with drastic changes in global climate, a major extinction of nektonic organisms, and major shifts in the carbon and oxygen isotope compositions of marine carbonates and phosphates. However, the timing of these events and their interrelationships remain controversial. Previous studies concluded that the latest Smithian-earliest Spathian interval was a time of extremely high temperatures, which would have precluded marine (macro)-vertebrates from inhabiting the equatorial realm. Conversely, based on oxygen isotope measurements of conodont elements collected at high temporal resolution from the Salt Range record (Pakistan), we report a major cooling event during that time interval. These results suggest that the interplay between climate and biodiversity patterns is more complex than usually portrayed.