Understanding the possible responses of Atlantic Meridional Overturning Circulation (AMOC) to climate warming is one of the major challenges of modern oceanography. Today, the lower (deeper) southward flowing limb of AMOC consists of the North Atlantic deep water (NADW), which is predominantly formed by deep water convection in the ocean basins to the north and south of Iceland. The southward transit of deep water formed in the northerly basins (Greenland-Iceland-Norwegian Seas) is constrained by gateway geometry to two major flow pathways to the east and west of Iceland. To the south of Iceland extensive deep-sea sediment archives, in the form of contourite drifts, are deposited by these currents and have provided critical information about AMOC and NADW dynamics through the Pleistocene. Here we make use of recently recovered cores from one of these sediment drifts (Gardar Drift, IODP Expedition 395, Site U1564,), that records the deep Iceland-Scotland Overflow water (ISOW) dynamics back to the warm climates states of the late Miocene to Pliocene. By combining sedimentological and X-Ray fluorescence derived elemental proxy evidence, we reconstructed deep ocean current activity and carbonate preservation between 5.0–6.2 million years ago (Ma). The record supports the periodic presence of deep currents since the latest Miocene, as well as a distinct ISOW weakening that coincided with the global warming trend, and the severe restriction on Mediterranean Outflow Water, just before the Miocene-Pliocene boundary. Low carbonate preservation hints to the presence of corrosive water masses in the North Atlantic following the termination of the Messinian salinity crisis.