Redox variations across the Permian-Triassic boundary (PTB) have long been debated, especially during the proliferation of PTB microbialites. Here, we report redox fluctuations across the PTB to evaluate links between the two based on pyrite framboid analysis from basin to platform settings in South China. During the end-Permian extinction, abundant framboids indicate a widespread anoxia that was likely a direct cause of extinction. In the earliest Triassic (Hindeodus parvus conodont zone), pyrite framboids were absent in ramp to basin and shallow, nonmicrobialite platform sections. In contrast, the coeval microbialites yield abundant framboids indicative of dysoxia. The fact that framboids were only confined to PTB microbialites and absent in other habitats indicates that microbe bloom may have stimulated dysoxic watermass and triggered the framboid growth within microbe aggregates. Thus, microbialites were not built in reducing settings, but instead, microbial proliferation caused local, dysoxia within shallow oxygenated platforms after the extinction.