Seaweeds are naturally abundant and spread all over the globe. They have several biologically active secondary metabolites of great interest. In this work, Sargassum muticum was the algae employed as biomass and the aim was to extract phenolic compounds (PCs) using eutectic solvents (ESs). Several betaine-based, proline-based, and choline-based ESs were tested for the extraction of PCs. All extracts were evaluated according to the total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity (DPPH). Afterwards, the extracts were characterized using HPLC in terms of 9 target PCs (gallic acid, 3,4-dihydroxybenzoic acid, caffeic acid, syringic acid, p-coumaric acid, ferulic acid, salicylic acid, catechin and quercetin). Proline combined with propylene glycol (Pro : PPG) exhibited a higher yield according to HPLC results, followed by proline : 1,2-butanediol (Pro : 1,2-But) and choline : citric acid (ChCl : CA). Pro : PPG also presented high selectivity towards salicylic acid, while ChCl : CA towards gallic acid. Optimization studies of water content and temperature were performed for the three best ESs, the optimum conditions being 30% (v/v) water and 60 °C extraction temperature. Ultrasound-assisted extraction (UAE) and microwave-assisted extraction (MAE) were two intensification methods evaluated to enhance the extraction process, proving their ability to reduce the extraction time when compared with the conventional solid–liquid extraction (SLE) process. In particular, Pro : PPG-based MAE provided a significantly higher extraction yield in comparison with conventional extraction and with the other extraction solvents. In summary, the combination of ESs with intensification techniques was shown to be a valuable valorization strategy of a marine macroalgae waste, in particular Sargassum muticum.