The control of the biodiesel production plays an important role on achieving the production standard of the biodiesel. The quality of the produced biodiesel depends on the raw materials, alcohol and catalyst selections and process and storage conditions. The control of the biodiesel production not only enables to achieve high quality biodiesel but also maintains the continuity of the product quality. In this work, an automation system for a two stage biodiesel production is designed and realized. A PLC (Programming Logic Control) based system is used for this purpose. The designed and realized biodiesel production facility enables to produce biodiesel using either a single stage or a two stage process. The quality of the biodiesels separately produced using a single stage and a two stage process are analyzed and compared. The analysis results show that a two stage biodiesel production process gives better results compared to the single stage in fuel density, viscosity and flash point