A system and method are provided for controlling temperature of a batch fermenter in a biofuel production process. A nonlinear predictive integrating temperature model for a batch fermentation process is provided that is a function of fermenter level. An objective for the batch fermentation process specifying a target fermenter temperature for the batch fermentation process is received, as is process information for the batch fermentation process, including fermenter level and fermenter temperature. The nonlinear predictive integrating temperature model is executed in accordance with the objective using the process information as input to determine target values for manipulated variables for controlling fermenter temperature of the batch fermentation process. The fermenter temperature for the batch fermentation process is controlled in accordance with the target values to produce biofuel in accordance with the objective, to substantially optimize the end of batch biofuel yield.