Global warming is causing rapid change in marine food webs, particularly at northern latitudes where temperatures are increasing most rapidly. In this study, the diet of common minke whales Balaenoptera acutorostrata was assessed both in terms of short-term (morphological analyses of digestive tract contents) and longer-term (tissue chemical markers: fatty acids and stable isotopes) prey use in the northern Barents Sea to see if they are prey shifting. Samples (blubber cores, muscle, and stomach contents) were obtained from 158 common minke whales taken during Norwegian commercial whaling operations during summer over the period 2016–2020. Two prey items, capelin Mallotus villosus and krill (primarily Thysanoessa sp.), dominated the stomach contents in the entire period of investigation, which included sampling both in June and in August, similar to findings from earlier studies. A few gadoids were also observed in the whale stomachs. Lower blubber fatty acid (FA) contents in 2016/2017 as compared with 2018/2019 were observed. This is most likely explained by differences in sampling time (June in 2016/2017 vs August in 2018/2019, i.e., after a longer feeding period during the summer in the latter case). This explanation also fits with the fact that FA profiles of the 2018/2019 whales were more similar to the FA profiles of the potential prey, presumably reflecting the two months longer assimilation time for these whales. Multidimensional mixing models based on carbon and nitrogen isotope composition of the most likely prey groups suggested that the whales ate mostly krill in four of the five sampling years. In 2018 there were indications of a higher proportion of gadoid fish, showing some dietary flexibility. The trophic level of the whales’ feeding, as interpreted from the nitrogen isotope values, was positively correlated with blubber thickness suggesting that fish-eaters tended to assimilate more energy than whales that focused more exclusively on lower trophic prey. The variation suggested by different dietary analyses methods − stomach contents, fatty acids, and stable isotopes – most likely reflects different turnover times, with muscle stable isotopes likely representing several months of dietary integration, while lipid stores are more dynamic and may represent weeks, and stomach contents represent feeding events during the last few hours. The change in diet of minke whales from small pelagic fishes (in the past) to a greater quantity of krill and demersal fish (seen in this study) suggests that the whales are responding to the ongoing borealization of the Barents Sea ecosystem.