We present authigenic neodymium isotope data (εNd) from two sediment cores from the Atlantic sector of the Southern Ocean (SO). The samples were prepared with a weak leach solution and measured with the ThermoFisher Neptuneplus MC-ICPMS at the Institute of Environmental Physics in Heidelberg. Both investigated sites are located south of the modern polar frontal zone within the modern mixing zone of Circumpolar Deep Water and Antarctic Bottom Water. The following data sets extend the data from Hallmaier et al. (2025) (https://doi.org/10.1594/PANGAEA.956277) far back to the Mid Pleistocene Transition. The Nd isotopic data from site ODP 1093 forms a continuous record from 150 ka to 1 Ma with a millennial resolution. It reveals a strong variability synchronous to the ice volume and thus the global climate with radiogenic glacial and unradiogenic interglacial values for the past 30 MIS. The measurements of the sediment from site ODP 1094 cover MIS 11-12 and the time around the 900 ka event. The data shows a transition from an unradiogenic signal of low variability prior to the 900 ka event to a highly variable signal for the time after.