The Laptev Sea plays an important role for sea ice formation in the Arctic Ocean, but very little is known about the biodiversity and ecosystem structure in this region. Sea ice dynamics in the Laptev Sea have undergone dramatic changes in the past decades, with negative trends in ice area and earlier ice retreat in summer. This in turn has led to increases in primary production observed by satellite measurements, which may result in higher carbon export fluxes from the surface to the seafloor. The effects of these changes on ecosystem structure and pelagic-benthic coupling are largely unknown. Here we investigated differences between benthic stations down the Laptev Sea continental slope (60-3400 m water depth) sampled two decades apart. Our results suggest that environmental changes in the past two decades have led to a substantial increase in phytodetritus availability at the seafloor along the entire transect, which is in contrast to hypotheses suggesting a decrease in carbon flux to the seabed as a potential result of increased zooplankton grazing in the water column. Bacterial communities play an essential role in carbon and nutrient cycling at the seafloor, and we therefore specifically investigated changes in their biomass, community structure and activity. While bacterial abundances (biomass) and overall community structure showed no systematic changes between the two years, extracellular enzymatic activities and to some extent also oxygen uptake had increased as a result of higher food availability. This indicates a direct effect of sea ice retreat and changes in primary production on the function of benthic microbial communities. Although the increase in bacterial community activity is not reflected in an increase of benthic bacterial standing stock, the response of larger benthic size classes remains unknown and would require additional comparative surveys. This study carried out in the framework of the ERC project ABYSS (no. 294757) reveals a close coupling between pelagic and benthic ecosystem processes in a region dramatically influenced by global change over a time frame of two decades.