Reduction of sea ice in the Arctic may significantly alter the relative fluxes of phytoplankton and ice algae to the seafloor. To examine the response of Arctic benthic communities to changing food supplies, we incubated sediment cores collected from two sites (Smeerenburg Fjord, northwest Svalbard in May 2003 and Storfjord Trench, Barents Sea in May 2004) with controlled additions of natural phytoplankton and ice algal assemblages, and laboratory-cultured 13C-labeled ice algae (Nitzschia frigida, in 2004 only). We measured sediment respiration, pigments, lipid biomarkers, and compound-specific δ13C signals over the course of incubations. Both communities responded rapidly to the addition of food materials: regardless of food type, concentrations of organic biomarkers (pigments and fatty acids) decreased to the levels of control cores within seven days. Although we found no evidence for selective ingestion of the different food types by macrofauna, fatty acids were differentially consumed. The enriched polyunsaturated fatty acids of the ice algae were preferentially utilized compared to saturated and monounsaturated fatty acids bound in ice algae. However, the saturated and monounsaturated fatty acids of phytoplankton (with depleted polyunsaturated fatty acids) are utilized more efficiently than those counterparts bound in ice algae. Bacterial activity was stimulated by food addition, indicated by the immediate increase of bacteria-specific fatty acids, but the direct assimilation of 13C-labeled carbon into bacterial biomass was limited. Our results imply that Arctic benthic communities can meet their energetic requirements by altering strategies to assimilate different components from variable food supplies.