Utilizing deep eutectic solvents (DESs) combined with microwave-assisted extraction (MAE) provides a sustainable method for extracting bioactive compounds from the macroalgae Ascophyllum nodosum and Laminaria hyperborea. Two DES formulations, choline chloride/lactic acid (ChCl/LA) and sodium acetate/lactic acid (AcNa/LA), were evaluated under varying extraction conditions. For L. hyperborea, ChCl/LA at 150 °C for 10 min yielded a total phenolic content (TPC) of 15.34 mg GAE/g DW, with antioxidant activities measured by DPPH (34.55 mg TE/g DW) and ABTS (27.06 mg TE/g DW). Extending the extraction to 20 min at 130 °C increased the TPC to 19.12 mg GAE/g DW. A. nodosum exhibited higher bioactivity, with the TPC reaching 47.51 mg GAE/g DW under the same conditions. High-performance liquid chromatography (HPLC) identified significant phenolics such as 3,4-dihydroxybenzoic acid (678.05 µg/g DW) and vanillin (6718.5 µg/g DW). Antimicrobial assays revealed strong inhibition (zones > 20 mm) against Clostridium perfringens, moderate activity against Staphylococcus aureus, and selective activity against Escherichia coli. FT-IR confirmed the presence of phenolics, polysaccharides, and lipids. Thermal and structural characterization revealed that A. nodosum residue showed an amorphous structure, while L. hyperborea retained crystallinity with decomposition profiles indicating potential bioenergy potential. SEM images revealed significant cell wall disruption correlating with extraction efficiency. These results demonstrate DES–MAE as an effective, green strategy for producing high-value algal extracts and valorizing residual biomass for biotechnological applications.