Interest in seaweed as a sustainable source of protein is growing, and deep eutectic solvents (DESs) are a promising green alternative with proven efficacy in protein extraction. This work studies the selective extraction of protein towards carbohydrates from the brown algae Saccharina latissima using DESs. Eleven DESs based on choline chloride (ChCl) and betaine were tested for freeze-dried biomass. The four DESs with the best performance (ChCl:Oxalic acid, ChCl:2Urea, ChCl:2Levulinic acid and Betaine:2Urea:Water) were subsequently used to investigate the effect of temperature (20, 30 and 40 °C) and the addition of water (0 and 47 %) on the extraction process. Betaine:2Urea:Water at 1 h, 40 °C, and 47 % added water provided the highest protein recovery yield (10.6 %) while minimizing carbohydrate extraction (1.3 %). These results demonstrated similar protein recovery yields to a benchmark process using bead milling, but with better selectivity. Thus, this work provides a sustainable extraction method for the recovery of proteins from seaweed and open new alternatives combining both approaches.