A method is disclosed for on-line prediction of performance of a fermentation unit, such as prediction of performance parameters like concentration of product, biomass, or sugar in the broth of a batch/fed-batch fermentation unit containing bacteria and nutrients. A computer model predicts a future product concentration based on current plant data. While a batch is in progress, model parameters are adjusted on-line based on plant data to reduce a mismatch between the plant data and model data. A method/fermenter model can be implemented as a software program in a PC that can be interfaced to a plant control system for on-line deployment in an actual plant environment. An on-line performance monitoring system can be used by plant operating personnel, to know the performance of the batch in advance for implementing corrective measures in advance to improve/maintain performance at desired level.