In this research, Candida rugosa lipase was used to produce fatty acid alkyl ester by interesterification reaction of palm oil with ethyl acetate or propyl acetate. The covalent immobilization of lipase on Fe3O4-polydopamine nanoparticles was prepared by coprecipitation methods. Magnetite (Fe3O4) was used in lipase immobilization because of its binding efficiency and selective separation under a magnetic field. The immobilized lipase and Fe3O4-polydopamine nanoparticles were characterized using FTIR, XRD, and FESEM-EDS. Immobilized lipase has 84.8% of loading percentage and 3.67 U/mg of specific activity, while free lipase has 13.09 U/mg of specific activity. All sample showed the high composition percentage of oleic acid alkyl ester. Conversion percentage of fatty acid ethyl ester from free and immobilized were 17.48% and 9.93%. Conversion percentage of fatty acid propyl ester from free lipase and immobilized lipase were 11.57% and 9.88%. Immobilized lipase on Fe3O4-polydopamine nanoparticles could be used up to three times reaction and has a decrease of relative activity by 72.4%.