Geochemical and isotopic data presented here cover the Paleocene-Eocene Thermal Maximum (~56 Ma ago) and were produced to assess the degree of carbon cycle perturbations, ocean acidification and the origin of the emitted carbon added to the atmosphere-ocean system during this major carbon cycle perturbation event. For further details on the analytical approach please refer to the original publication (Gutjahr et al., 2017, Nature). Data contained within the two tables comprise foraminiferal carbonate based stable boron, carbon and oxygen isotopic results from DSDP Site 401 located within the Bay of Biscaye in the NE Atlantic (Table 1). This table also contains B/Ca, Mg/Ca and Al/Ca data from the same samples. Depth in core is presented alongside two alternative relative age models setting ages in relation to the Carbon Isotope Excursion observed during the Paleocene Eocene Thermal Maximum. Table 2 contains high-resolution bulk carbonate stable carbon and oxygen isotopic results that were produced to establish a new age models for this core.