A pacemaker having a motion sensor is configured to set atrial event sensing parameters used for sensing atrial systolic events from a motion signal produced by the motion sensor. The pacemaker sets at least one atrial event sensing parameter by identifying ventricular electrical events and setting a sensing window following each of the ventricular electrical events. The pacemaker may determine a feature of the motion signal produced by the motion sensor during each of the sensing windows and set the atrial event sensing parameter based on the determined features.