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Macroalgae are one of the most environmentally friendly resources, and their industrial by-products should also be sustainable. Algal polysaccharides represent valuable products, and the definition of new eco-sustainable extraction processes, ensuring a safe and high-quality product, is a new goal in the context of reducing the carbon footprint. The aim of the present work was to determine the influence of the extraction methodology on the properties and structure of the polysaccharides, comparing conventional and innovative microwave-assisted methods. We focused on extraction times, yield, chemical composition and, finally, biological activities of raw polymers from three macroalgal species of Chlorophyta, Rhodophyta and Phaeophyceae. The main objective was to design a sustainable process in terms of energy and time savings, with the aim of developing subsequent application at the industrial level. Extraction efficacy was likely dependent on the physico-chemical polysaccharide properties, while the use of the microwave did not affect their chemical structure. Obtained results indicate that the innovative method could be used as an alternative to the conventional one to achieve emulsifiers and bacterial antiadhesives for several applications. Natural populations of invasive algae were used rather than cultivated species in order to propose the valorization of unwanted biomasses, which are commonly treated as waste, converting them into a prized resource.