Chaetognaths (arrow worms) are important components of zooplankton communities in terms of abundance, biomass and contribution to carbon export. Though traditionally considered strict carnivores, recent studies have identified “omnivorous” chaetognaths. These may feed on non-animal materials, including algae, detritus or sediments. The feeding strategies of the Arctic species Eukrohnia hamata and Parasagitta elegans are particularly interesting given differences in their vertical distributions, and the strong seasonality (peaks and troughs) in the abundance of expected prey items, such as copepods. We analyse the feeding history of these chaetognaths in the Beaufort and Chukchi Seas, and Baffin Bay, using gut contents (types and colours) as short-term signals (days), and biochemistry (stable isotope, lipid and fatty acid composition) as signals integrated over the longer-term (weeks to months), to investigate seasonality in diets and determine the extent to which animal and non-animal matter are consumed. Between November 2007 and July 2008 in the Beaufort Sea, green detritus and oil droplets were abundant in the guts of only E. hamata and were found to contain evidence of diatoms. Weak differences in apparent predation rates and prey items for the two species, but high amounts of green detritus and silica in E. hamata guts point towards direct ingestion of diatoms and marine snow at both epi- and meso-pelagic depths, and can explain δ15N and δ13C-contents that may predict omnivory in the Chukchi Sea and Baffin Bay (fall 2014). Dietary signals in P. elegans predict that this species has a reduced dependence on diatom source pathways relative to E. hamata, for instance a relative absence in green material in guts, and a lower 16:1 (n − 7) concentration. Whilst nitrogen isotopes and fatty acid biomarkers suggested a more carnivorous diet, they also suggest that Calanus copepods are less important to its diet than other types of zooplankters. We suggest that E. hamata (whether pelagic or hyper-benthic) likely receives a substantial energy input from algae and detritus and is thus not a strict carnivore. Our data provide the stimulus for continued focus on these organisms and the important role they play in carbon flux as we try to better understand carbon cycling in a changing Arctic Ocean.