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The Cultivation of “Saccharomyces cerevisiae” for enzyme production was monitored using Near-infrared spectroscopy. An inline NIR optrode was therefore immersed in a 15 L vessel. The calibration was done using a Partial Least Squares (PLS) model with reference measurements of glucose, ammonium, phosphate, ethanol, and optical density. A nonlinear biological process model based on an extended Kalman Filter (EKF) was used to describe the fermentation behavior. It was found that EKF corrects inaccurate PLS predictions.