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This study pertains to the selection of the appropriate process parameters of lipid extraction aimed at the valorization of sea-bass gutting and filleting side stream biomass. A comparative kinetic study between an environmentally friendly polar (ethanol) and a conventional non-polar solvent (hexane) was implemented to determine the effect of temperature, solvent to solid ratio and time, providing insights in terms of the yield recovery and quality of omega-3 fatty acids. Maximum recovery yield (43.8 and 34.0 g/100 g of dried gutting and filleting by-products, respectively) was achieved within 10 min. In gutting by-products, ethanol achieved full lipid recovery at 35 °C and a 50:1 ratio, while for hexane, the maximum yield was 83%. In the case of filleting side-streams, hexane achieved exhaustive recovery at a 50:1 ratio and 20 °C compared with ethanol, where a higher temperature (50 °C) was needed for exhaustive recovery to be achieved. Differences were attributed to the diverse fatty acid profiles among the two by-products, with 27.3% and 40.8% polyunsaturated fatty acids in viscera and fish frames, respectively. All extracts at 20 °C and 35 °C remained below the oxidation limit set by the Codex Alimentarius Commission (peroxide value < 5 <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mrow><mi mathvariant="normal">m</mi><mi mathvariant="normal">e</mi><mi mathvariant="normal">q</mi></mrow><mrow><msub><mrow><mi mathvariant="normal">O</mi></mrow><mrow><mn>2</mn></mrow></msub></mrow></msub><mo>/</mo><msub><mrow><mi mathvariant="normal">k</mi><mi mathvariant="normal">g</mi></mrow><mrow><mi mathvariant="normal">o</mi><mi mathvariant="normal">i</mi><mi mathvariant="normal">l</mi></mrow></msub></mrow></semantics></math></inline-formula>; p-anisidine value < 20). Therefore, green solvents could assist conventional extraction, combining high efficiency and an improved environmental impact.