Electronic tongues (ETs) based on potentiometric sensor arrays are often used for foodstuff classification, origin recognition, estimation of complex samples' properties, etc. In the last few years they were also applied for various fermentation monitoring, such as Aspergillus niger fermentation, light cheese production, batch Escherichia coli fermentation, as a devices capable of fast, inexpensive, automated and on-line control of the process. In this work a novel application for ET is proposed-flow-through array of solid state electrodes was used for the analysis of samples obtained during methane fermentation (anaerobic digestion) of whey in sequencing batch bioreactor, according to their volatile fatty acid (VFA) content and chemical oxygen demand (COD).