Microalgae are a promising source of high-quality nutrients for the growing population. They contain high concentrations of protein, unsaturated fatty acids and carbohydrates, as well as vitamins and antioxidants. However, conventional separation methods are too high in cost or cause contamination in the end product. Thus, fungal bioflocculation has gained traction as a promising separation method. This is a process in which microalgae adhere to mycelial surfaces. Problematically, previous studies often investigated the bioflocculation process via inedible and possibly harmful fungal species. In this study, the safe and edible fungus Aspergillus oryzae was investigated for the bioflocculation of marine microalga Tetraselmis subcordiformis on the basis of agricultural residues. Fungal growth conditions were optimized to achieve a maximum separation of 99.5% and dry mass ratio (algal to fungal) of 0.48 g g−1. This efficacy was achieved with the fungal culture conditions of 25 °C, 75 rpm, 105 spores mL−1 and an addition of 800 mg L−1 urea. Additionally, field emission scanning electron microscopy and microscopy of thin sections of paraffin embedded biomass revealed that the mycelial structure played a critical role in microalgal separation. The nitrogen addition resulted in a denser mycelial network, aiding the capture of microalgal cells, thus enhancing bioflocculation. Overall, the above-described process was able to produce biomass suitable for human consumption while exclusively utilizing agricultural residues as media components. These findings open possibilities for scalable, cost-effective microalgae harvesting systems, which can be integrated into sustainable food production. Future research could focus on optimizing the system for other microalgal species and exploring industrial scale applications in food and feed sectors.