The main objective of this study was to investigate how the freshness of saithe (Pollachius virens) viscera affected the quality, composition and yield of oil obtained by silaging. Minced viscera with and without liver were stored separately for up to 3 days at 4 °C before silaging at pH 3.8 for 6 days at 10 °C. An antioxidant mixture was added to evaluate the effect on the lipid oxidation. Oil was extracted thermally from untreated raw material during storage (day 0–3) and after silaging. For oil obtained after silaging of viscera with liver, the oil yields increased significantly when the raw material was stored for more than one day prior to the treatment. Use of fresh raw material (collected at day 0) led to significantly lower oxidation compared to longer raw material storage. After one day of storage, the oxidation was less dependent on the freshness. Silaging with antioxidants resulted in significantly lower formation of oxidation products compared to acid without antioxidants and the most significant differences were observed after one day of storage. Contents of docosahexaenoic acid (DHA) and total omega-3 fatty acids decreased significantly when the raw material was stored for 1–3 days prior to silaging compared to fresh raw material. Results obtained by high resolution nuclear magnetic resonance (NMR) spectroscopy indicated that oxidation of esterified DHA might explain the DHA decrease. The free fatty acid content was highest when fresh raw material was used and was most likely affected by the formation of cholesteryl esters observed in NMR spectra after longer storage. The study shows that although the oil quality is reduced during silaging, processing shortly after catch and use of antioxidants can optimize the quality resulting in less oxidized oil richer in omega-3 fatty acids.