Palm olein (POL) was enzymatically interesterified in a continuous packed bed reactor (PBR). The effects of interesterification parameters (flow rates of 4.5–40 g/min and temperatures of 50–90 °C) on the properties of interesterified fats and immobilized Thermomyces lanuginosus lipase (Lipozyme ® TL IM) were investigated. Generally, the percentage of saturated fatty acid at sn-2 remained along with higher flow rates (acyl migration inhibited), while the percentage increased along with higher temperatures and lower flow rates (acyl migration promoted). Solid fat content and crystallization rate of the interesterified fats also showed significant modification with the reaction parameters since these properties are directly influenced by the shift in the triacylglycerol compositions. The occurrence of hydrolysis was also evident during the early stage of interesterification attributed to the lipase's water content, which diminished over time as the water concentration decreased. Under prolonged reaction, the lipase's catalytic activity reduced from 236 U to 65 U, and significant changes in the protein's secondary confirmation were observed. After 100 h of reaction, the α-helix structure decreased (from 23.37% to 16.82%) while β-pleated sheet increased (28.10%–39.59%). The increased fluorescence intensity reflected a significant change in the lipase's tertiary structures.