During the Palaeocene-Eocene Thermal Maximum (PETM) about 56 million years ago, thousands of petagrams of carbon were released into the atmosphere and ocean in just a few thousand years, followed by gradual sequestration over approximately 200,000 years. If silicate weathering is one of the key negative feedbacks that removed this carbon, a period of seawater calcium carbonate saturation greater than pre-event levels would be expected during the event's recovery phase. In marine sediments, this should be recorded as a temporary deepening of the depth below which no calcite is preserved - the calcite compensation depth (CCD). Previous and new sedimentary records from sites that were above the pre-PETM CCD show enhanced carbonate accumulation following the PETM. A new record from an abyssal site in the North Atlantic that lay below the pre-PETM CCD shows a period of carbonate preservation beginning about 70,000 years after the onset of the PETM, providing the first direct evidence for an over-deepening of the CCD. This record confirms an overshoot in ocean carbonate saturation during the PETM recovery. Simulations with two earth system models support scenarios for the PETM that involve a large initial carbon release followed by prolonged low-level emissions, consistent with the timing of CCD deepening in our record. Our findings indicate that sequestration of these carbon emissions was most likely the result of both globally enhanced calcite burial above the CCD and, at least in the North Atlantic, an over-deepening of the CCD.