Display omitted •Better fabrication and modification methods of magnetic materials were identified.•The optimized Fe3O4@Arg can achieve 95% harvesting efficiency.•The optimal method has a low cost of 347 USD/t of algal biomass harvested.•The amino-acid content and the amino group number play roles in better harvesting. Harvesting is a critical step in microalgae-based biodiesel production. Oleaginous microalgae harvesting by magnetic nanomaterials has gained attention because of the advantages of higher efficiency, lower cost, and convenient operation. In the present study, Fe3O4 magnetic nanoparticles (MNPs) were fabricated using two different methods (chemical coprecipitation and thermal decomposition), modified with amino acid using three different approaches (ultrasonic, long-time mixing, and “one-step” approaches), and utilized for oleaginous microalgae Chlorella sp. HQ harvesting. The results showed that the Fe3O4 MNPs synthesized by the chemical coprecipitation method achieved superior performance when considering both harvesting efficiency and fabrication cost. For the amino-acid modification, the one-step approach outcompeted the other approaches. At a dosage of 200 mg/L, the optimized Fe3O4@Arginine MNPs could achieve a harvesting efficiency of 95% with a low cost of only 347 USD/t of harvested algal biomass. Both the amino-acid content on the NPs and the number of amino groups in the amino acid molecules played a role in improving the harvesting performance.