A mathematical model was developed for the oxidation of glycerol with Gluconobacter oxydans as a tool for process design. The kinetics of this fermentation process were evaluated by respiratory activity measured on line by mass spectrometry. Glycerol did not inhibit product formation but the product, dihydroxyacetone, damaged the cells irreversibility. Such damaged cells were nonviable but catalytically active, which made it necessary to describe a Gluconobacter culture as consisting of two types of cells. A structured segregated mathematical model was developed based on kinetic measurements. This was able to simulate the dynamic behaviour of batch and fed batch fermentations with good agreement with measured concentration profiles.