This dataset compiles raw measurements generated to investigate perturbations of the marine nitrogen cycle during the Paleocene–Eocene Thermal Maximum (PETM). It includes abundances of isoprenoidal GDGTs (isoGDGTs) and crenarchaeol mass accumulation rates, (ii) chromatographic peak areas of bacteriohopanetetrol (BHT) and BHT-x, and (iii) the nitrogen isotopic composition of bulk sediments (bulk sediment δ¹⁵N). Samples were collected from multiple ocean basins and regions: the Central Arctic Ocean (IODP 302–M0004), East Tasman Plateau in the Southwest Pacific (ODP Site 1172), Central Northern Caucasus (Kheu River), the New Jersey Shelf/Atlantic Coastal Plain (ODP 174AX Ancora), the Côte d'Ivoire–Ghana Transform Margin in the equatorial Atlantic (ODP 959), the Southeast Newfoundland Ridge in the central North Atlantic (IODP 1403), Fur Island, Denmark (Fur Formation), and the Tarim Basin, western China (Qimugen Formation). Lipid biomarker data were obtained using liquid chromatography coupled to mass spectrometry, and bulk nitrogen isotope data were measured by elemental analysis coupled to isotope-ratio mass spectrometry.