This work reports bioconversion of unsaturated free fatty acids present in soapstock, inherent waste of edible oil manufacture, to the epoxidized fatty acids using Candida rugose lipase in a micro-reactor. Activation energy of the epoxidation reaction was found to be 32.27 kJ mol−1 while the enzyme deactivation was observed at higher temperature than 35 °C with an activation energy of 91.18 kJ mol−1. The low hydrodynamic retention time in the micro-reactor provides a proper condition to measure of initial rates of the enzymatic reaction. The kinetics study was performed at ten different molar ratios of H2O2/C=C, and constants of the Ping-Pong bi bi model were estimated as follows: the maximum specific enzyme activity (Vmax) of 1.453 × 105 mM min−1 genzyme−1, dissociation constant for enzyme-FFA complex (KA) of 58.83 mM genzyme−1, Michaelis constant for FFAs (KmA) of 1.382 × 103 mM genzyme−1, Michaelis constant for hydrogen peroxide (KmB) of 3.279 × 106 mM genzyme−1, and the deactivation constant due to hydrogen peroxide (KIB) of 59.25 mM genzyme−1. The cross-linked enzyme aggregate technology provided a simple method to produce the robust biocatalyst for this bioconversion where more than 89% of original activity was maintained after 9 cycles in the micro-reactor.