Harvesting costs, accounting for 15–30 % of total expenses, are a major bottleneck in microalgae biorefinery due to low cell density and energy-intensive processes. This study investigates Fe3O4-Urea (Fe@urea) nanocomposites (NCs) to replace conventional methods and improve the harvesting efficiency (HE) of Chlorella zofingiensis, known for its high lipid and astaxanthin content. Urea-coated magnetite nanoparticles (NPs) with additional functional groups significantly improved harvesting performance across all pH levels compared to conventional Fe3O4 NPs. HE was evaluated using both optical density and cell counting methods, with the latter proving superior results by eliminating interference from unreacted salts and debris. Optimization of nanocomposite concentrations and culture pH with Fe@urea achieves 95 % HE at 800 mg L−1 and pH 3–4. The Langmuir and Freundlich models confirmed the nanocomposite's multifaceted capabilities. Characterization techniques included SEM, FTIR, EDX, zeta potential analysis, and TEM. This innovative approach can revolutionize large-scale microalgae biorefineries, enhancing sustainable biofuel and bioproduct production and supporting the Sustainable Development Goal of Affordable and Clean Energy (SDGs 7).