A micro refinery system includes a fermentation tank, a distillation tube and a membrane ethanol separation mechanism. A batch that includes sugar, yeast and water is mixed in the fermentation tank. Sensors detect the physical characteristics of the batch and the operating status of the system. The sensors are coupled to a control system that compares the detected processing information to a look up table to determine if the system is operating under optimum ethanol productivity conditions. If the sensors detect a problem with the batch, the control system can add chemical components to the batch to correct the chemical imbalance. The system can also facilitate remote operations by transmitting sensed information to an operator computer and receiving control commands from the operator computer.