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Understanding the changes in, and drivers of, isotopic variability of sulfur in seawater sulfate (delta S-34(SO4-sw)) over geological time remains a long-standing goal, particularly because of the coupling between the biogeochemical sulfur and carbon cycles. The early Cenozoic has remained enigmatic in this regard, as the existing seawater sulfate isotopic records appear to be decoupled from the well-defined carbon isotope composition of the ocean. Here, we present a new Cenozoic record of sulfur isotopes, using carbonate-associated sulfate hosted in the calcite lattice of single-species foraminifera. The vastly improved stratigraphy afforded by this record demonstrates that carbon and sulfur cycles, as recorded by their isotopes, are not fully decoupled in the early Cenozoic. With a model driven by partial coupling of the carbon and sulfur cycles, we demonstrate that a change in sulfur isotopic fractionation of the pyrite burial flux best explains the large increase in delta S-34(SO4)-sw similar to 53 million years ago (Ma) and the subsequent long steady state. We suggest that the locus of pyrite burial changed from shallow epicontinental seas and shelf environments to more open-ocean sediments around 53 Ma. Loss of extensive shelf environments corresponds to Cretaceous-Palaeogene sea-level changes and tectonic reorganization, occurring as the Himalayan arc first collided with Asia.