Through the transfer of carbon from the surface to the deep ocean via the passive sinking and active transport of organic material, the biological pump is a key global process for the regulation of atmospheric CO2. Over the last decades, studies relying on sediment traps and other bio-devices moored over an annual cycle in the Arctic Ocean helped to resolve how the Arctic biological pump is operating and how it is responding to global change. Here, we provide a short review of the pioneer work done in the 1980-90’s and we present key knowledge gained on Arctic ecosystem functioning with a series of case-studies conducted in the 2000’s on the basis of bio-moorings: (1) carbon export in response to warm anomalies in the main Arctic gateway, the Fram Strait; (2) ecosystem-level analyses in Beaufort Sea from a vertical flux perspective; (3) the importance of lateral processes for sinking flux events in the Central Basin; and (4) the impact of zooplankton life-cycle strategies on the biological pump in fjord-like systems. We also identify regional challenges and potential future research avenues in terms of new sampling tools and coordination for the development of an Arctic biogeochemical observatory network aligned with global initiatives. As such, this paper represents a call to sustain and further develop observing activities that rely on bio-mooring arrays in the Arctic Ocean over the next decade. By capturing the full seasonality of ice-covered environments, we argue that bio-moorings are one of the most powerful approaches to distinguish natural variability from actual shifts that might affect the structure and function of Arctic marine ecosystems in response to human-induced changes.