A practical problem that limits the development of miniaturized multi-ion sensors is the definition of the various ion-sensitive membranes located in close proximity to each other. In this paper a glass-based flow-through cell containing four ISFETs is presented. The ISFETs are connected to the cell by means of anodic glass bonding, thus defining 200 μm deep, 500 μm diameter micropools around the ISFET gates. The individual ion-sensitive membranes for calcium and potassium ions and pH are solvent cast into these micropools, ensuring a good separation and thus a minimal crosstalk between the different membranes. A fourth ISFET is covered with a diffusion delaying hydrogel and acts as a reference for the three ion sensors. The cell, with an internal volume as small as 12 μl, is evaluated in connection with a FIAstar® flow injection analysis system.