A leading hypothesis for lower atmospheric CO2 levels during glacial periods invokes increased ocean stratification with a corresponding shift of dissolved inorganic carbon and nutrients from intermediate depths to deep waters. If the rapid deglacial rise in atmospheric CO2 (∼17–10 ka) were caused by a breakdown of this stratification and increased ventilation of deep water masses, then one consequence would be increased CaCO3 preservation in deep sea sediments. We present down core records of CaCO3 preservation for the last 21,000 years from 31 cores in the tropical and subtropical Pacific, Atlantic and Indian Oceans. Our preservation records are based on a multi-proxy approach involving a new CaCO3 dissolution proxy (the Globorotalia menardii Fragmentation Index), size normalized foraminifer shell weights and 230Th-normalized CaCO3 accumulation rates. In some cores our proxy records add to the growing body of evidence in support of the hypothesized breakdown of glacial stratification. However, in most cores the expected deglacial increase in CaCO3 preservation is missing. Accepting that the deglacial hypothesis is well supported by other evidence, here we explore processes and conditions that erased the expected CaCO3 signal from our records including: (1) variations in the ratio of organic carbon to CaCO3 flux in the eastern equatorial Pacific, (2) very low sedimentation rates and bioturbation in the western equatorial Pacific and (3) increased northward penetration of Antarctic Bottom Water in the equatorial Atlantic.