Three kinds of biodiesel production processes are compared and it is shown that the microwave heated acid process has higher productivity than the conventional heating alkaline or acid processes. The reaction time to reach the maximum yield in microwave-irradiated process is reduced to 50% of the time required by conventional heating processes. An optimization of process variables was done to identify the optimum microwave process irradiation. Searching an explanation for this non thermal microwave effect, a statistical design to stablish the complete chemical kinetic equation for soya oil transesterification with ethanol catalyzed by methane sulfonic acid was realized. The kinetical results show that this process has a complex mechanism that can be seen as a pseudo-1.6 global order reaction with low activation energy. Precisely, the order is 0.004 with respect to ethanol and -1.6 to soya oil. An analysis of this negative order was done and it brings a little more information to understand how to get best returns from biodiesel operations.