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In this study, the effect of a four-stage chemical refining process (degumming, neutralization, bleaching, deodorization) on the quality parameters, fatty acid composition and volatile compounds of crude oils produced from processing by-products of farmed fish species (tuna, seabass and gilthead seabream) was evaluated. The quality of the oils was compared to commercially available cod liver oil on the basis of free fatty acid, peroxide value, p-anisidine, total oxidation (TOTOX), thiobarbituric acid reactive species (TBARS), oxidative stability at 80, 100 and 120 °C, tocopherol content, and volatile components, while the fatty acid profile and the proportion of polyunsaturated fatty acids (PUFAs) were used as an indicator of the nutritional values of fish oils. Quality parameters of the studied oils and oil oxidative stability were enhanced with refining and were within the limits recommended for fish oils without the loss of PUFAs. In tuna by-product refined oils, the proportion of PUFAs was over 40%, with 30% of eicosapentaenoic and docosahexaenoic fatty acids. The volatile compounds of the oils were quantified (in mg/kg) and major components were 2,4-heptadienal, pentadecane, 2,4-decadienal, 2,4-nonadienal and dodecane. The use of aquaculture by-products as an alternative source for fish oil production could contribute to a more sustainable and profitable aquaculture production, providing economic benefits for the producers and setting new standards for a fish by-product disposal strategy.