Undaria pinnatifida, an invasive brown macroalgal species found along European coasts, was studied for valorization through the sustainable extraction of pharmaceutically active biomolecules. The recovery of the health promoting xanthophyll fucoxanthin (Fx) from Wakame was maximized using a combined environmentally friendly approach, involving the bio-based and green ionic liquid (IL) cholinium-L-lysinate and supercritical carbon dioxide. Pre-treatment conditions were kept constant at room temperature with 2% IL loading, while extraction pressure and temperature in the supercritical extractor cell were varied for optimization. A maximum Fx yield of 0.133 mg/g dry alga was achieved at 40 ◦C and 600 bar and at 25 ◦C and 700 bar without IL pretreatment, with the extraction time kept constant at 240 min. In contrast, IL pre-soaked seaweed showed an Fx extraction yield of 0.351 mg/g alga at 60 ◦C and 400 bar, representing an improvement of more than 2.5-fold, confirming the hypothesis that chemical cell wall disruption with cholinium-L-lysinate results in improved Fx yields. Replicate extraction runs confirmed the reproducibility of the combined approach with a coefficient of variation of 7.18%. Furthermore, response surface methodology analysis validated these findings, showing that both approaches, with and without IL  pre-treatment, provided statistically significant predictions of the Fx yield, while in comparison the IL-assisted model demonstrated enhanced reproducibility and greater predictive accuracy.