This study aimed to evaluate the antioxidant activity of bioactive compounds extracted from Gracilaria gracilis cultivated in an integrated multi-trophic aquaculture (IMTA) system by different extraction solvents and to investigate the potential capacity of the extracts in cellular systems against environmental pollutants. The global yields, total polyphenol contents, and antioxidant activity were assessed on G. gracilis by DPPH radical scavenging activity, comparing the antioxidant extraction efficiency of the different solvents (ethanol 80%, acetone 70%, N-hexane, and water). Ethanol extract, granted by the highest extractive yield and antioxidant capacity, was tested in vitro in the Sparus aurata fibroblast (SAF-1) cell line to evaluate its protective role against oxidative stress induced by the chemical flame retardant 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47). The results demonstrate that the cells pretreated with G. gracilis extract were protected against oxidative stress and had improved cell viability, cellular antioxidant defense system, and cell cycle control, as demonstrated by the gene expression on some biomarkers related to the cell cycle (p53) and oxidative stress (nrf2, sod, and cat). These results confirm that bioactive compounds obtained from seaweeds cultivated in IMTAs could contribute to producing high-value ingredients that are able to counteract environmental stressors, for the growth of the marine biobased industrial sector and the expansion of new value chains.