In this study, the intracellular lipases of Candida catenulata were examined as a whole-cell biocatalyst (WCB) of soybean oil transesterification and obtained a fatty acid methyl ester (FAME) yield of 79.1%. To facilitate the biocatalyst recovery and improve its stability, the WCB was attached to magnetic Fe3O4 nanoparticles activated by a linear structure of polyethyleneimine (PEI) as the multi-amino-functionalized arm. The preparation procedure of the magnetic whole-cell biocatalysts (MWCBs) was optimized by considering the pH during immobilization (X1), the weight ratio of nanoparticles-to-cell (X2), and PEI concentration (X3) using the response surface methodology. The best optimal setting of the variables was determined at X1 of 6.1, X2 of 0.6, and X3 of 0.7 w% with the transesterification activity of 7.6 × 105 IU gbiocatalyst−1 gained a FAME yield of 78.4% after 3 h. The MWCBs showed an improvement in thermal stability where the optimal temperature was shifted from 34C to 38 °C and the deactivation energy was increased from 183.9 kJ mol−1 and 223.6 kJ mol−1 after the immobilization. The MWCBs displayed satisfactory sustainability in the repeated transesterification experiments and maintained 87.3% of the original activity after 10 cycles which was higher than the bare-WCB system with a recovery of 57.4%.