System and method for managing a biofuel production process. An integrated dynamic multivariate predictive model is provided that includes a continuous process model representing a continuous process of the biofuel production process, a batch process model representing a batch process of the biofuel production process, and a continuous simulation framework. The batch process model interacts with the continuous process model as a nonlinear continuous process via the framework using bridging equations. An objective is received, as is constraint information specifying constraints for the biofuel production process, where the constraints are in terms of the framework, and process information related to the batch and continuous processes. The integrated model is executed per the objective using the process information as input, generating target values for variables related to the batch and continuous processes per the objective and subject to the constraints, and used to control the batch and continuous processes substantially optimally.