The valorization of side streams from fishery and aquaculture value-chains is a valuable solution to address one of the challenges of the circular economy: turning wastes into profit. Side streams produced after filleting of sea cage fattened bluefin tuna (Thunnus thynnus) were analyzed for proximate composition and fatty acid profile to evaluate the possibility of producing tuna oil (TO) as a valuable source of ω-3 polyunsaturated fatty acids (PUFA) and testing its bioactivity in vitro. Ethyl esters of total fatty acids (TFA), obtained from TO, were pre-enriched by urea complexation (PUFA-Ue) and then enriched by short path distillation (SPD) up to almost 85% of the PUFA fraction (PUFA-SPe). The bioactivity of TFA, PUFA-SPe, and ethyl esters of depleted PUFA (PUFA-SPd) were tested in vitro, through analysis of lipid metabolism genes, in gilthead sea bream (Sparus aurata) fibroblast cell line (SAF-1) exposed to oils. TFA and PUFA-SPd upregulated transcription factors (pparβ and pparγ) and lipid metabolism-related genes (D6D, fas, fabp, fatp1, and cd36), indicating the promotion of adipogenesis. PUFA-SPe treated cells were similar to control. PUFA-SPe extracted from farmed bluefin tuna side streams could be utilized in fish feed formulations to prevent excessive fat deposition, contributing to improving both the sustainability of aquaculture and the quality of its products.