The Paleocene–Eocene transition was a time of short-term rapid climatic and biotic change, superimposed on a long-term warming trend. The response of shallow tropical carbonate systems to past rapid warming is important to understand in the context of ongoing and future anthropogenic global warming. Larger benthic foraminifera (LBF) were abundant and important components of shallow water ecosystems throughout the early Paleogene and are sensitive to environmental change, making them ideal organisms to track shallow marine biodiversity. Furthermore, through the use of integrated bio- and chemostratigraphy it is possible to correlate the shallow (<100 m) and deep water realms to create a regional stratigraphic framework for the time period. Here we present a new LBF biostratigraphic and high-resolution carbonate carbon isotopic record spanning the Paleocene–Eocene transition from the onshore sub-surface of the United Arab Emirates (UAE). Results show a turnover event in the LBF assemblage during the early Eocene, whereby there are a number of first and last occurrences of species over this interval. However, assemblages remain generally stable coincident with the large negative carbon isotope excursion interpreted to be the onset of the Paleocene–Eocene thermal maximum (PETM). Turnover in the LBF assemblage in the early Eocene likely occurred due to the crossing of a long-term climatic and oceanographic threshold. The impacts of this long-term climatic change on the overall biotic assemblage at this site are significant, with LBF outcompeting a previously diverse community of corals, gastropods, and bivalves to become the dominant carbonate producers through the Paleocene–Eocene transition. Despite this, modern studies suggest that LBF are not immune to impacts of anthropogenic climate change, perhaps due to the significantly higher rates of change in the modern compared to the Paleocene–Eocene transition.