In this work, lipase from Candida rugosa was bound with the multi-covalent bonds attachment to the amino-functionalized magnetic Fe3O4 nanoparticles by glutaraldehyde as a coupling agent. The protein assay showed that the enzyme binding efficiency was 77.65% in the immobilization process. The catalytic activity of the immobilized lipase was compared with the free lipase in enzymatic epoxidation of free fatty acids. The results showed that the immobilized enzyme had better stability than the free system during the reaction in the presence of hydrogen peroxide, as an inactivating substrate, especially at extreme conditions of temperature and pH. The statistical study on effects of temperature and pH by response surface methodology specified that the highest epoxidation activity for the immobilized system was observed at temperature 52.2 °C and pH of 6.7. At the optimum condition, the immobilized lipase showed a good reusability, where 100% and 80.97% of origin catalytic epoxidation activity were, respectively, maintained after sixth and tenth cycles. Also, the storage stability of the immobilized lipase was investigated in room temperate and 4 °C. The experiments revealed that the immobilized lipase had an excellent long-term storage stability after 152 and 203 days at 4 °C after being bound to magnetic nanoparticles.