A system for controlling the position of a diaphragm in a diaphragm-containing pressure pod, is provided. The system can include a peristaltic pump, a pressure pod having a flow-through fluid side and a gas side that are separated by a diaphragm, and a pressure sensor operatively connected to the gas side. The pressure sensor is configured to sense pulses of pressure resulting from movement of the diaphragm and caused by the action of the peristaltic pump. A gas source and a valve can be in fluid communication with the gas side of the pressure pod and can be configured to provide gas to, or vent gas from, the gas side. A controller receives pressure signals from the pressure sensor and controls the valve in response, and in so doing, controls the position of the diaphragm. Methods for positioning the diaphragm are also included.