In this work, superparamagnetic Fe3O4 nanoparticles were synthesized by chemical co-precipitation using ionic liquid of 1-Butyl-3-methylimidazolium tetrafluoroborate ([BMIN] BF4) as templates. Then, the magnetic Fe3O4 nanoparticles were treated with 3-aminopropyltriethoxysilane (APTES) and obtain the surface amino-functionalized magnetic nanoparticles (APTES-Fe3O4) were used as immobilization material. Lipase was covalently bound to the APTES-Fe3O4 magnetic nanoparticles by using glutaraldehyde as a coupling reagent. A fatty acid methyl ester (FAME) conversion of 89.4% could be achieved by lipase immobilized on APTES-Fe3O4 magnetic nanoparticles under optimized conditions of methanol-oil molar ratio of 6: 1, with a catalyst dose of 20%, 2% water content and 250 rpm agitation speed at 45 degrees C for 24 h. The FAME conversion remained greater than 70% even after reusing the catalyst for 5 reactions. In addition, the lipases immobilized on APTES-Fe3O4 magnetic nanoparticles could be recovered easily by external magnetic field for further use.