Microalgae are increasingly recognized as renewable biofactories for producing high-value bioactive molecules. However, their industrial exploitation is limited by their rigid cell walls, metabolite heterogeneity, and the energy-intensive nature of the extraction processes. Recent advances in process-intensification technologies, including microwave-assisted, ultrasound-assisted, enzymatic, pressurized liquid, and supercritical CO₂-based methods, have significantly improved extraction efficiency and selectivity, with reported lipid recoveries exceeding 40–50% in some microalgal systems and carotenoid recoveries approaching 90% under optimized conditions. NADES-assisted systems further enhance mass transfer and solubilization through tailored hydrogen-bonding interactions, enabling selective extraction of polar and semi-polar metabolites under mild conditions. However, limitations remain, including high viscosity, variability in extraction performance, and challenges in solvent recovery and scale-up. This review critically evaluates the extraction efficiency, mechanistic basis, and sustainability of NADES-assisted processes, highlighting key limitations and identifying research priorities for their integration into scalable microalgal biorefinery systems.