Arctic sea ice is a critical component of the climate system as it influences the albedo, heat, moisture and gas exchange between ocean and atmosphere as well as the ocean's salinity. An ideal location to study natural sea ice variability during pre-industrial times is the East Greenland Shelf that underlies the East Greenland Current (EGC), the main route of Arctic sea ice and freshwaters from the Arctic Ocean into the northern North Atlantic. Here, we present a new high-resolution biomarker record from the East Greenland Shelf (73°N), which provides new insights into the sea ice variability and accompanying phytoplankton productivity over the past 5.2 kyr. Our IP25 based sea ice reconstructions and the inferred PIP25 index do not reflect the wide-spread late Holocene Neoglacial cooling trend that follows the decreasing solar insolation pattern, which we relate to the strong influence of the polar EGC on the East Greenland Shelf and interactions with the adjacent fjord throughout the studied time interval. However, our reconstructions reveal several oscillations with increasing/decreasing sea ice concentrations that are linked to the known late Holocene climate cold/warm phases, i.e. the Roman Warm Period, Dark Ages Cold Period, Medieval Climate Anomaly and Little Ice Age. The observed changes seem to be connected to general ocean atmosphere circulation changes, possibly related to North Atlantic Oscillation and Atlantic Multidecadal Oscillation regimes. Furthermore, we identify a cyclicity of 73–74 years in sea ice algae and phytoplankton productivity over the last 1.2 kyr, which may indicate a connection to Atlantic Multidecadal Oscillation mechanisms.