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The Permian−Triassic mass extinction, the most severe biotic crisis of the Phanerozoic, has been linked to environmental perturbations triggered by the eruptions of the Siberian Traps Large Igneous Province. However, several of these perturbations have previously been demonstrated to have started several hundred thousand of years before the main extinction phase. To explore this timing and its ecological implications, we analyzed molecular fossils across the Permian−Triassic transition in two shallow marine carbonate ramp sections in the tropical Tethys Ocean of the Dolomites (northern Italy). Both the shallower (Siusi/Seis) and the deeper (Seres) settings record a sudden increase in polycyclic aromatic hydrocarbons, including pyrene and coronene, just above the extinction interval. These compounds probably originated from the combustion of organic-rich sedimentary rocks during Siberian Traps sill emplacement and were subsequently distributed across the study area. Redox-sensitive and source-indicative molecular fossil indices, such as pristane/phytane (Pr/Ph), the terrigenous-aquatic ratio, and (Pr + Ph)/(n-C17 + n-C18), reveal that redox conditions, the input of terrestrially derived organic matter, and the relative abundance of photoautotrophs were more variable in the shallower than in the deeper setting. This variability suggests that ecosystems in shallow restricted environments underwent more volatile changes than those in deeper settings. The shallower setting therefore records the effects of ubiquitous sea level fluctuations rather than an early onset of the environmental crisis preceding the extinction event, highlighting spatial heterogeneity in ecosystem responses and underscoring the importance of regional environmental context when interpreting extinction dynamics.