Geochemical records generated from the calcite tests of benthic foraminifera, especially those of the genera Cibicidoides and Uvigerina, provide the basis for proxy reconstructions of past climate. However, the extent to which benthic foraminifera are affected by postdepositional alteration is poorly constrained. Furthermore, how diagenesis may alter the geochemical composition of benthic foraminiferal tests, and thereby biasing a variety of proxy-based climate records, is also poorly constrained. We present the Foraminiferal Preservation Index (FPI) as a new metric to quantify preservation quality based on objective, well-defined criteria. The FPI is used to identify and quantify trends in diagenesis temporally, from late Pliocene to modern coretop samples (3.3–0 Ma), as well as spatially in the deep ocean. The FPI identifies the chemical composition of deep-ocean water masses to be the primary driver of diagenesis through time, while also serving as a supplementary method of identifying periods of changing water mass influence at a given site. Additionally, we present stable isotope data (δ¹⁸O, δ¹³C) generated from individual Cibicidoides specimens of various preservation quality that demonstrate the likelihood of significant biasing in a variety of geochemical proxy records, especially those used to reconstruct past changes in ice volume and sea level. These single-test data further demonstrate that when incorporating carefully selected tests of only the highest preservation quality, robust paleorecords can be generated.