Lipid decomposition of saithe (Pollachius virens) light and dark muscles was monitored during frozen storage at −25 °C of raw (up to 18 months) and cooked products. Samples were cooked after 0, 6 and 12 months raw storage then refrozen and stored at −25 °C for 12 months to determine the stability of cooked-then-stored samples. Fatty acid profiles, formation of hydroperoxides (PV), thiobarbituric acid reactive substances (TBARS), fluorescence compounds (OFR) and free fatty acids (FFA) were evaluated throughout the storage for all samples. In general, results indicated that enzymatic lipolysis was the driving factor influencing the quality of saithe over raw storage and it mostly affected polyunsaturated lipids in the light muscle. Cooking, however, inhibited FFA formation and induced formation of PV and TBARS. This behavior was more evident in samples cooked after long raw storage periods. The initial quality of the raw material before cooking is therefore critical with regard to oxidative stability of cooked fish products.