We have thus employed a commercially available professional microwave (MW) reactor in a continuous flow process instead of conventional batch MW units, with the aim to provide the guideline for the development of large-scale process for biodiesel production. The FlowSynth (from Milestone, Italy) has been used as the continuous-flow microwave reactor in this work. MW heating has been proven to enhance heat transfer in the transesterification process [15]. It uses the polarity of some compounds to transform electromagnetic energy to heat. The magnitude of heating depends only on the dielectric properties of the molecules. This produces thorough uniform heating throughout reacting media. MeOH has a dielectric constant (ε) of around 33 and is a suitable media in which to produce biodiesel in an MW assisted reactor. Unlike conventional heating for biodiesel production, heat transfer mainly occurs via convection from the heating surface to the bulk reaction mixture. It does not only cause non-uniform heating but also requires a long heating time.