The major Cenozoic shift from a shallow (∼3–4 km) to deep (∼4.5 km) calcite compensation depth (CCD) occurred at the Eocene-Oligocene Transition (∼34 Ma), suggesting a strong relationship between calcium carbonate (CaCO₃) cycling and Antarctic glaciation. However, the linkages between these two events are debated. Here we present new records of bulk sediment stable isotope and carbonate composition from a depth transect of sites in the low-latitude Pacific Ocean and one site from the South Atlantic Ocean, together with a new benthic foraminiferal stable isotope record (δ¹³Cb and δ¹⁸Ob) from the Pacific where the sedimentary sequence is most expanded. Our records reveal a short-lived (∼300 Kyr) CCD shoaling event closely associated with a negative carbon isotope excursion in the latest Eocene. This event is immediately followed by CCD deepening which occurs in two rapid (∼40 Kyr-long) steps. Our data show that the first of these deepening steps represents recovery from the latest Eocene shoaling event while the second was closely associated with a rapid increase in δ¹⁸Ob and shows a distinctive over-deepening and settling pattern to >5 and 4.4 km, respectively. These results, together with good agreement between Pacific and South Atlantic records, strongly suggest that the carbon cycle was perturbed globally shortly before the inception of Antarctic glaciation. Once large-scale Antarctic glaciation was initiated, rapid further change in global seawater chemistry triggered transitory deep ocean carbonate burial fluxes far exceeding their early Oligocene steady state values.