Near-infrared spectroscopy (NIRS) is known to be a rapid and non-destructive technique for process monitoring. Bioprocesses are usually complex, from both the chemical (ill-defined medium composition) and physical (multiphase matrix) aspects, which poses an additional challenge to the development of robust calibrations. We investigated the use of NIRS for on-line and in-line monitoring of cell, substrate and product concentrations, during aerobic and anaerobic bacterial fermentations, in different fermentation strategies. Calibration models were built up, then validated and used for the automated control of fermentation processes. The capability of NIR in-line to discriminate among differently shaped bacteria was tested.