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Significant amounts of marine raw material are lost on-board the deep-sea vessels due to fast quality degradation. Optimal on-board handling and processing strategies can upgrade these resources from waste to food ingredients rich in nutrients such as omega-3 fatty acids. The objective of this study was to investigate the effect of raw material freshness and sorting on the quality, composition and yield of oil produced thermally from cod (<i>Gadus morhua</i>) residuals on-board a commercial trawler. Oil was produced from whole viscera fractions with liver or out-sorted livers right after a catch and after chilled storage for up to 6 days. The results showed that significantly higher oil yields could be obtained if the raw materials were stored for 1 day or longer. However, an undesired emulsion was formed when viscera were stored for 4 days. All oils were rich in health beneficial omega-3 fatty acids, but viscera oils had generally lower quality with higher levels of free fatty acids and oxidation products. However, out-sorting of the liver was not necessary to meet guidelines for high-quality fish oil. Both viscera and liver could be stored for up to 2 days at 4 °C prior to oil production and still meet quality criteria for food applications. These results demonstrate a large potential in upgrading currently wasted marine raw materials into high-quality food ingredients.