Microalgae are esteemed for their potential as sustainable sources of bioactive compounds, notably astaxanthin, a valuable antioxidant with diverse health applications. This study investigates Fe3O4 nanoparticle efficacy in harvesting astaxanthin-producing microalgae for sustainable applications. Parameters such as nanoparticle concentration, exposure time, and magnetic field strength were optimized for Haematococcus pluvialis and Chlorella zofingiensis biomass harvesting. Fe3O4 nanoparticles achieved >99% harvesting efficiency in H. pluvialis at 200 mg L-1 across all pH ranges, while C. zofingiensis showed peak efficiency at 800 mg L-1 and pH 4. The zeta analyzer revealed a maximum potential gap at pH 4, facilitating stable binding of microalgae with nanoparticles. This research underscores Fe3O4 nanoparticles’ sustainable harvesting potential, aligning with Sustainable Development Goals SDGs such as Industry, Innovation, and Infrastructure (SDG 9) and Responsible Consumption and Production (SDG 12). It offers a promising pathway for industrial-scale microalgae production and astaxanthin exploitation, with implications for biorefinery development, and commercialization in pharmaceuticals, nutraceuticals, and cosmetics industries.