During the late Pliocene global climate changed drastically as the Northern Hemisphere glaciation (NHG) intensified. It remains poorly understood how the North Atlantic Current (NAC) changed in strength and position during this time interval. Such changes may alter the amount of northward heat transport and therefore have a large impact on climate in the circum-North Atlantic region and the growth of Northern Hemisphere ice sheets. Using the alkenone biomarker we reconstructed orbitally resolved sea surface temperature (SST) and productivity records at Integrated Ocean Drilling Project (IODP) Expedition 306 Site U1313 during the late Pliocene and early Pleistocene, 3.68–2.45 million years ago (Ma). Before 3.1 Ma, SSTs in the mid-latitude North Atlantic were up to 6 °C higher than the present and surface water productivity was low, indicating that an intense NAC transported warm, nutrient-poor surface waters northwards. Starting at 3.1 Ma, surface water characteristics changed drastically as the NHG intensified. During glacial periods at the end of the late Pliocene and beginning of the Pleistocene, SSTs decreased and surface water productivity in the mid-latitude North Atlantic increased, reflecting a weakened influence of the NAC at our site. At the same time the increase in surface productivity suggests that the Arctic Front (AF) reached down into the mid-latitudes. We propose that during the intensification of the NHG the NAC had an almost pure west to east flow direction in glacials and did not penetrate into the higher latitudes. The diminished northward heat transport would have led to a cooling of the higher latitudes, which may have encouraged the growth of large continental ice sheets in the Northern Hemisphere.