In recent years it has become apparent that the “cool tropic paradox” of Paleogene and Cretaceous “greenhouse” climates arises because of the diagenetic alteration of tropical planktic foraminiferal calcite near the seafloor, yielding artificially high δ ¹⁸O values. Because the Mg/Ca compositions of foraminiferal and inorganic calcite are thought to be quite different, Mg/Ca measurements should be a sensitive way of monitoring diagenetic alteration. Here we examine the extent of diagenetic alteration of Eocene planktic foraminiferal calcite using scanning electron microscope imaging of foraminiferal test microstructures and geochemical (δ ¹⁸O and Mg/Ca) analyses. We compare microstructural and geochemical characteristics between given species exhibiting two contrasting states of preservation: those that appear “frosty” under reflected light and those that appear “glassy.” Microstructural evidence reveals extensive diagenetic alteration of frosty foraminiferal tests at the micron scale, while δ ¹⁸O analyses document consistently higher δ ¹⁸O (and therefore lower paleotemperatures) in this material. Yet we find that δ ¹⁸O offsets between species in these frosty foraminiferal assemblages appear to be generally preserved, suggesting that frosty foraminifera remain valuable for generating relatively short (approximately ≤1 Myr) paleoceanographic time series that do not demand absolute estimates of paleotemperature. We also find that the observed increase in Mg/Ca for planktic foraminifera exhibiting diagenetic alteration (compared to glassy taphonomies) is far smaller than would be expected from the addition of inorganic calcite based on laboratory-derived Mg²⁺ partition coefficients. Our findings imply that a much lower Mg²⁺ partition coefficient controls inorganic calcite formation in deep sea sedimentary sections, in accordance with the findings of Baker et al. (1982).