In the Arctic Ocean sea ice volume and extent currently experience massive reduction due to global warming. These rapid changes may have unforeseen consequences for pelagic biodiversity and biogeochemistry, particularly CO2 sequestration by the biological carbon pump. The production and export of carbonate-bearing organisms from the surface ocean can influence effective CO2 sequestration. However, the impact of rising temperatures and changing ice conditions on the export of carbonate-bearing organisms remains poorly constrained. Here we use sediment trap records to describe biogenic carbonate flux in relation to total matter flux and the export of foraminiferans, pteropods and ostracods. Samples were obtained from two sites: the Long-Term Ecological Research (LTER) observatory HAUSGARTEN in seasonally ice-covered eastern Fram Strait (since 2000), and over one annual cycle in the almost entirely ice-covered Nansen and Amundsen Basins (2011-2012). The flux of carbonate shell-bearing organisms showed large variations seasonally and annually at both Fram Strait and in the Central Arctic Ocean (CAO). Whereas the flux of foraminiferans was comparable at both sites, pteropod flux was high in the Fram Strait and negligible in Nansen and Amundsen Basin pointing towards a higher share of aragonite flux on total carbonate flux in the Fram Strait than in the CAO. Total matter and carbonate export flux were about one order of magnitude lower in the CAO compared to the eastern Fram Strait. Together, these results suggests that the two regions are characterized by different ecosystems and export mechanisms. The Fram Strait is changing from a partially seasonal ice-covered region towards an ice-free region with strong pelagic production and might provide valuable insights to the future of a summertime ice-free CAO.