In the Arctic Ocean, increased sea surface temperature and sea ice retreat have triggered shifts in phytoplankton communities. In Fram Strait, coccolithophorids have been occasionally observed to replace diatoms as the dominating taxon of spring blooms. Deep-sea benthic communities depend strongly on such blooms, but with a change in quality and quantity of primarily produced organic matter (OM) input, this may likely have implications for deep-sea life. We compared the in situ responses of Arctic deep-sea benthos to input of phytodetritus from a diatom (Thalassiosira sp.) and a coccolithophorid (Emiliania huxleyi) species. We traced the fate of 13C- and 15N-labelled phytodetritus into respiration, assimilation by bacteria and infauna in a 4-day and 14-day experiment. Bacteria were key assimilators in the Thalassiosira OM degradation, whereas Foraminifera and other infauna were at least as important as bacteria in the Emiliania OM assimilation. After 14 days, 5 times less carbon and 3.8 times less nitrogen of the Emiliania detritus was recycled compared to Thalassiosira detritus. This implies that the utilization of Emiliania OM may be less efficient than for Thalassiosira OM. Our results indicate that a shift from diatom-dominated input to a coccolithophorid-dominated pulse could entail a delay in OM cycling, which may affect benthopelagic coupling.