The negative carbon isotope excursion (CIE) associated with an ancient global warming event referred to as the Paleocene Eocene thermal maximum (PETM, ca. 56 Ma) is commonly observed to have a smaller magnitude in marine records than in terrestrial records. This disparity has been attributed to secondary mechanisms that either attenuate or amplify the CIE magnitude in marine and terrestrial records, respectively. Here we investigate the effects of carbonate diagenesis and sediment mixing on the stratigraphic signature of the CIE in a PETM record recovered at Ocean Drilling Program (ODP) Site 1135 in the southern Indian Ocean. Comparison of parallel planktic foraminifer δ13C records constructed with two different analytical techniques – conventional gas source mass spectrometry (GSMS) measurements of individual whole shells versus in-situ microanalyses on subdomains inside individual foraminifer shells using secondary ion mass spectrometry (SIMS) – shows that both the δ13CGSMS and δ13CSIMS records capture the CIE. However, the δ13CSIMS records yield excursion magnitudes (acarininids = 5.3‰, morozovellids = 3.9‰) that are ~1.6‰ larger than in the whole-shell δ13CGSMS records. Patterns of intrashell δ13C variation delineated by the in-situ SIMS microanalyses indicate that the smaller CIE magnitude registered by δ13CGSMS records is chiefly due to incorporation of diagenetic calcite overgrowths by GSMS analyses of whole foraminifer shells. We also find that many foraminifer shells are infilled with fine-fraction carbonate (nannofossils) and posit that incorporation of non-CIE nannofossils into these infillings further bias whole-shell GSMS δ13C measurements toward more positive values over the CIE interval. We propose that 5.3‰ is the best estimate of the CIE in this deep-sea record, a near match to the average CIE magnitude published for terrestrial PETM records.