This dataset contains the seasonal composition of intact phospholipids as well as of free fatty acids from the digestive system of Antarctic krill, Euphausia superba. Krill was caught with a continuous krill pumping system in May of 2021 in the Bransfield Strait and in January and March of 2022 at the South Orkney Islands. The stomach, digestive gland and hind gut were dissected and analysed individually. Samples were extracted with an optimized Bligh&Dyer protocol. Intact phospholipids were measured with liquid chromatography - high-resolution mass spectrometry on an Orbitrap mass spectrometer. Identification of intact phospholipids was based on characteristic fragments of the head group in MS2 experiments in positive electrospray ionization mode, while the fatty acid composition of intact phospholipids were determined by characteristic fragments occurring during MS2 measurements with negative electrospray ionization. Free fatty acids from the total lipid extract were measured as methyl esters were via gas chromatography - mass spectrometry and identified with standards and based on their retention order.