Himanthalia elongata (HE), commonly named sea spaghetti, is a brown alga from the order Fucales, mainly found in the North Atlantic Ocean and in the Baltic and North Seas. This algae is currently used in numerous functional applications in the food, pharmaceutical and nutraceutical industries, due to its biological properties such as antioxidants, anti-inflammatory, antimicorbial and anticancer and other health benefits. These effects are reported to be attributed to the high content of nutrients and their secondary metabolites such as phenolic compounds. In this context, the objective of this study is to optimize the microwave-assisted extraction method (MAE) to recover phenolic compounds and flavonoids, taking into account three extraction parameters: the ethanol concentration in water (0-100%), the extraction time (3-25 minutes) and the pressure (2-20 bar). In order to verify the total phenolic content (TPC) and the total flavonoid content (TFC), two biological tests were carried out based on the radical scavenging activity 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the antioxidant capacity trolox equivalent (TEAC). Subsequently, the optimization was carried out by response surface methodology (RSM) considering the performance (Y) of each fraction. Finally, the optimized MAE parameters were fixed at 16.01 ± 4.80 min, 20 ± 0.50 bar and 0% of ethanol. These results show that water is an ideal environmenally friendly solvent for the extraction of bioactive HE compounds with some beneficts from a industrially point of view due to its nature. Furthermore, the resulting RSM was a successful model to establish the optimal conditions of MAE and a suitable methodology to maximize the content of polyphenols and total flavonoids, as well as the antioxidant capacity and the SM extraction performance.