The possibility of monitoring state transitions during the time course of a fermentation through the analysis of the on-line collected near-infrared (NIR) spectra with sample-sample two-dimensional correlation spectroscopy (SS-2DCoS) was investigated. SS-2DCoS has proved to be useful for extracting process information directly from the spectra collected on-line. The complexity of the system studied prevented the extraction of concentration profiles, but nevertheless, the application of SS-2DCoS enables the identification of fermentation state transitions due to metabolic and morphological changes of the microorganism.