Intensification of chemical processing using microwave irradiation reduced energy and the processing time requirement. Present work investigated the synthesis of fatty acids methyl esters (FAME) from renewable feedstock Calophyllum inophylum Linn. A two-step acid esterification followed by an alkali transesterification protocol was employed for FAME synthesis due to the initial higher amount of free fatty acid content in feedstock and to avoid saponification during the second step. Batch-scale experiments were performed to gain useful data for the development of a continuous reactor. Performance of batch and continuous reactors was analyzed based on oil-methanol ratio, catalyst concentration, and processing time. Continuous operation required marginally higher processing time and oil-methanol ratio compared to batch operation. FAME yield was nearly the same for both methods. The optimum results for batch esterification were 1:3 oil-methanol molar ratio, 1.5% catalyst concentration, and reaction time 20 min, and for batch transesterification, 1:6 oil-methanol molar ratio, 1.0% catalyst concentration, and reaction time 15 min. Similar results were obtained for the continuous process at an optimum flowrate of 6 mL/min. The properties of FAME, such as density, kinematic viscosity, and flash point, were compatible with ASTM D6751. Shortfalls of microwave reactors, such as low penetration depth, associated hotspots, and the internal geometry of the microwave cavity. It can be overcome using tubular-type microwave reactors. The promising results presented will be useful for the continuous reactor development. Reactors can be scaled up to any scale by increasing tube length.