Calanus finmarchicus is a marine zooplankton of interest for the aquaculture industry, as well as for nutraceuticals and the cosmetic industry. The chemical composition of C. finmarchicus rapidly changes postmortem due to autolytic processes; in particular phospholipids rapidly degrade to give free fatty acids. The aim of this study was to inactivate autolytic enzymes in C. finmarchicus by applying heat (72°C, 5-30min) through mixing with boiling, fresh water, and further to explore the effects of heat (70°C, 15min) combined with long time storage (-20°C, 12months) of treated and untreated material. Heat treatment (5min) inactivated all tested enzymes and maintained the initial amount of phospholipids, total lipids and crude protein. Storage of untreated material led to complete degradation of all phospholipids, whereas heat treatment resulted in a stable product containing the initial amount of phospholipids and astaxanthin.