Microalgae have received significant attention as promising resources for biodiesel. However, the downstream processes for the production of biodiesel, which range from cultivation, harvesting, dewatering, and lipid extraction to oil upgrading, are economically impracticable and can be improved. Therefore, efficient microalgal harvesting and integrated technologies are required to realize microalgae-based biodiesel. Herein, tri-functional (cationic, magnetic, and lipophilic) carbon microparticles filled with magnetite (Fe3O4) are synthesized through one-step aerosol spray pyrolysis and applied in microalgal harvesting and serial microalgal lipid entrapment. Carbon microparticles are tri-functional in the following respects: (i) the cationic carbon microparticles facilitate flocculation with anionic microalgae due to electrostatic attractions; (ii) the magnetic properties of the carbon microparticles, owing to embedded magnetites, enable the separation of microalgal flocs from low concentration cultures (similar to 2 gL(-1)) with a separation efficiency of 99%; and (iii) the lipophilicity enables the recovery of lipid droplets extracted from oleaginous microalgae. Microalgal lipids are directly separated through adsorption onto magnetic carbon microparticles from concentrated microalgal slurries after harvesting. The tri-functionality may facilitate the integrated use of magnetic carbon microparticles in microalgal biorefineries and the tri-functional microparticles could potentially be applied in various areas such as biomedicine, catalysis, magnetism, energy materials, and environmental remediation.