Microwaves for organic synthesis are widely used due to the fact that reaction times are reduced with product conversion and selectivity improved. In this work, transesterification was carried out continuously to obtain biodiesel. A control system adapted to a home microwave oven was developed, by automating the process for continuous flow and with the less operator intervention. An embedded system and virtual instrumentation created in LabVIEW platform, for activation/deactivation orders and monitoring data supported by a PIC 18F4550 microcontroller was developed. The operative part is a power interface of transistors and activators formed by relays. The temperature sensor and power stage of the operative part of the process were linked through a PC interface by using an algorithm for data acquisition. Communication and control of the system was made through the LabVIEW platform in order to monitor, in real time, the parameters required to obtain the product. Results of automation and performance are presented.