Phlorotannins from the brown macroalga Durvillaea antarctica (Cochayuyo) are recognized for their antioxidant, anti-inflammatory, and enzyme-inhibitory properties, making them promising compounds for nutraceutical and cosmetic applications. However, their recovery is challenged by the alginate-rich cell matrix and the susceptibility of these phenolics to oxidation and structural degradation during extraction. This study evaluated the mechanistic release and preservation of phlorotannins using two cell disruption strategies: hydroalcoholic treatment (70% ethanol) and mild alkaline hydrolysis (0.07 M NaOH). Hydroalcoholic extraction promoted cell matrix swelling and selective solubilization of native polymeric phlorotannins through favorable polarity and hydrophobic interactions. The highest phlorotannin concentration was obtained at 7 g biomass per 100 mL solvent, reaching 2.5 mg/mL while maintaining structural integrity and minimizing oxidative polymerization. In contrast, alkaline treatment increased cell wall disruption but also favored phenolic deprotonation and quinone formation, processes associated with phlorotannin oxidation and reduced recoverability. Consequently, the maximum concentration achieved with NaOH was 1.2 mg/mL at 6–7 g biomass per 100 mL. The environmental performance of both approaches was assessed through the E-factor. The ethanol-based process exhibited substantially greater eco-efficiency, with an E-factor of 3.24 compared with 55.46 for alkaline hydrolysis, indicating significantly lower waste generation and a more sustainable extraction profile. Although ethanol presents volatility considerations, these can be effectively managed under controlled operating conditions. Overall, hydroalcoholic disruption proved to be a more effective and environmentally favorable strategy for recovering intact phlorotannins from Durvillaea antarctica, supporting its application in sustainable macroalgal biorefinery processes.