The Siberian Traps flood basalts have been invoked as a trigger for the catastrophic end-Permian mass extinction. Widespread aberrant plant remains across the Permian-Triassic boundary provide evidence that atmospheric stress contributed to the collapse in terrestrial diversity. We used detailed estimates of magmatic degassing from the Siberian Traps to complete the first three-dimensional global climate modeling of atmospheric chemistry during eruption of a large igneous province. Our results show that both strongly acidic rain and global ozone collapse are possible transient consequences of episodic pyroclastic volcanism and heating of volatile-rich Siberian country rocks. We suggest that in conjunction with abrupt warming from greenhouse gas emissions, these repeated, rapidly applied atmospheric stresses directly linked Siberian magmatism to end-Permian ecological failure on land. Our comprehensive modeling supplies the first picture of the global distribution and severity of acid rain and ozone depletion, providing testable predictions for the geography of end-Permian environmental proxies.