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The proportional integral derivative (PID) controllers are widely applied in industrial process owing to their simplicity and effectiveness for both linear and nonlinear systems, and the tuning methods still a hot research area to give the optimum result for control behavior. Fuzzy logic and proportional integral derivative (PID) controllers are designed and compared for use in control on-line an advanced biodiesel microwave reactor system which converts waste cooking oil into biodiesel by transesterification chemical process. A closed loop fuzzy and PID controllers are used to automatically and continuously adjust the applied power of microwave reactor under different perturbations. Labview based software tool will be presented and used for measurement and control of the full system, that will make charts real time display as well as state real time monitoring.