This dataset contains planktonic foraminiferal counts and derived relative abundances from IODP Site 306-U1313, located in the central North Atlantic Ocean northeast of the Azores Islands (41°0.08'N, 32°57.4'W; 3426 m water depth). The record spans Marine Isotope Stages (MIS) 39 to 44 during the Early Pleistocene. Planktonic foraminiferal assemblages were analyzed in the >150 μm size fraction, including the 150–250 μm fraction when applicable. Taxonomic counts were performed on splits containing a minimum of approximately 300 specimens per sample. Species identification follows the taxonomic concepts of Schiebel and Hemleben (2017) and the Mikrotax database (Young et al., 2017). The dataset includes raw species counts and the corresponding relative abundances (%) calculated from the total planktonic foraminiferal assemblage. The age model is based on correlation of the planktonic δ¹⁸O record of Globigerina bulloides to the high-resolution isotope record from IODP Site 339-U1385. These data document changes in planktonic foraminifera assemblages during successive glacial and interglacial intervals of the Early Pleistocene.