A system and method are provided for managing batch fermentation in a biofuel production process. A nonlinear control model of yeast growth and fermentable sugar concentration for biofuel (e.g., fuel ethanol) production in a batch fermentation process (pure and/or fed-batch fermentation) of a biofuel production process is provided. Process information for the batch fermentation process is received, and the nonlinear control model executed using the process information as input to determine values of one or more fermentation process variables for the batch fermentation process, e.g., fermentation temperature and/or enzyme flow, for substantially maximizing yeast growth and achieving target fermentable sugar concentrations. The batch fermentation process is then controlled in accordance with the determined values for the one or more fermentation process variables to substantially maximize yeast growth and achieve target fermentable sugar concentrations, where substantially maximizing yeast growth and achieving target fermentable sugar concentrations substantially maximizes biofuel production in the batch fermentation process.