We report a label-free infrared surface plasmon biosensor with a double-chamber flow cell for continuous monitoring of morphological changes in cell culture exposed to various stimuli. In this technique, the monolayer of cultured cells is divided into two halves by a barrier, allowing the treatment of one half while the other serves as control. We demonstrate the advantages of this setup in test experiments that track kinetics of the IEC-18 cell layer response to variations in extracellular Ca2+ concentration. The sensitivity of the presented method was found to be an order of magnitude higher compared to the single-chamber biosensor.