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A setup for online fermentation monitoring was tested with suspensions containing yeast cells. A flow cell was equipped with a horizontal attenuated total reflection (ATR) unit for measurements of mid-infrared spectra. The stopped flow principle was employed to separately assess the liquid and the dispersed cells: dissolved components in the supernatant can be assessed while pumping the fermentation broth through the flow cell. Upon stopping the flow the culture can be monitored as the microorganisms settle onto the horizontal ATR diamond. Due to the surface sensitivity of ATR spectroscopy cleanness of the optical element is of particular importance. For yeast fermentations the formation of biofilms on the ATR surface was identified as limitation in regard to long-term stability. Initial experiments showed that the effective removal of residues was impossible by rinsing with water or a NaHCO3 solution. Therefore, various cleaning agents (2%) have been tested for their ability to clear off the biofilm. The problem of biofilm formation was additionally addressed by the exploitation of forces exerted on suspended particles within an ultrasonic standing wave (USW). The USW ( ~2 MHz) was built up between the ATR element and an ultrasonic transducer facing it. This technique of ultrasonic particle manipulation was applied to actively lift the sedimented material from the ATR after the infrared measurement, thus have the rinsing stream carry it away more effectively. Among the studied reagents surfactants and oxidizing agents showed to be most effective, the use of an USW was found to be feasible to remove a biofilm.