This dataset contains energy content measurements performed on zooplankton collected in the Arctic Ocean during the MOSAiC expedition (PS122) from November 2019 untill September 2020. Energy content measurements were done on Apherusa glacialis, Themisto abyssorum, Chaetognatha, Thysanoessa longicaudata and Calanus hyperboreus. These species are all known prey of polar cod (Boreogadus saida), and their energy content was measured to be included in a bioenergetic model of the growth rate of this predator and to gain insight in the differences between prey species. The meaurements were performed on freeze-dried specimens using a 6725 semi-micro oxygen calorimeter (Parr, USA) connected to a 6772 calorimetric thermometer (Parr, USA).