A cardiac rhythm management system includes an atrial pacing preference (APP) filter for promoting atrial pacing. The APP filter includes an infinite impulse response (IIR) or other filter that controls the timing of delivery of atrial pacing pulses. The atrial pacing pulses are delivered at an APP-indicated pacing rate that is typically at a small amount above the intrinsic atrial heart rate. For sensed beats, the APP indicated rate is increased until it becomes slightly faster than the intrinsic atrial heart rate. The APP-indicated pacing rate is then gradually decreased to search for the underlying intrinsic atrial heart rate. Then, after a sensed atrial beat, the APP filter again increases the pacing rate until it becomes faster than the intrinsic atrial rate by a small amount. As a result, most atrial heart beats are paced, rather than sensed. This decreases the likelihood of the occurrence of an atrial tachyarrhythima, such as atrial fibrillation. The decreased likelihood of atrial tachyarrhythmia, in turn, decreases the likelihood of inducing a ventricular arrhythmia, either as a result of the atrial tachyarrhythmia, or as the result of delivering a defibrillation shock to treat the atrial tachyarrhythmia.