Biofuels, such as biodiesel, are good for the environment because they add fewer emissions to the atmosphere than petroleum-based fuel. Conventional biodiesel processes are mainly based on use of high power thermal heating to produce biodiesel from pure or waste feedstock such as virgin vegetable oils or waste cooking oils. The development of a novel continuous microwave biodiesel reactor for the conversion of waste oil and fats into biodiesel is reported. This process has the capability to enhance the production of biodiesel in a very short time as compared with conventional methods that require lengthy hours and clays. Real time monitoring and control process in microwave biodiesel reactor is necessary to adjust the applied power of microwave reactor under different perturbations for the process temperature control, and full system real time monitoring. The paper focuses on an artificial intelligence technique to design online genetic-ANFIS temperature control based on LabVIEW. The designed controller was compared with error-based Adaptive controller to explore the robustness of the proposed controller in nonlinear real time application. Crown Copyright (C) 2012 Published by Elsevier Ltd. All rights reserved.