Arctic Ocean sea-ice cover is shrinking due to warming. Long-term sediment trap data show higher export efficiency of particulate organic carbon in regions with seasonal sea-ice compared to regions without sea-ice. To investigate this sea-ice enhanced export, we compared how different phytoplankton communities in seasonally ice-free and ice-covered regions of the Fram Strait affect carbon export and vertical dispersal of microbes. In situ collected aggregates, combined with microbial source tracking revealed that larger aggregates from sea-ice and under-ice diatom blooms were responsible for higher export efficiency and vertical microbial connectivity. During early summer, Phaeocystis aggregates dominated the ice-free regions and exported two-fold less carbon than diatom aggregates in ice-covered regions, and also less surface-born microbial clades to the deep-sea. This suggests that continuous ice-loss will further decrease pelagic-benthic coupling, impacting the quantity and quality of food input due to formation of slow-settling aggregates, with potential repercussions for Arctic deep-sea ecosystems.