A new method of the integration of ion-sensitive membrane and silicon sensor chip has been developed. The ion-sensitive membrane is deposited into pyramidal containments produced on silicon by an anisotropic etching technique. Here we demonstrate the application of this method to the development of nitrate-sensitive sensors and ammonium-sensitive sensors. Acrylate and silicon matrix membranes were casted into the membrane containment. The sensors showed comparable response characteristics like sensors with PVC matrix membranes but had a considerably improved yield of sensor preparation.