A method and system are provided for controlling an adaptive pacing therapy using an implantable medical device (IMD). The method provides electrodes that are configured to be located proximate to an atrial (A) site, left ventricular (LV) site and right ventricular (RV) site of the heart. The method utilizes one or more processors to perform obtaining an intra-atrial conduction interval (IACI-LVPROX) between an atrial event and intrinsic conduction at an LV site that is proximal to a sinoatrial (SA) node and obtaining timing of a first heart sound S1. The processors determine whether the S1 occurs after the IACI-LVPROX, and calculates an S1-conduction lag ΔS1_C between the IACI-LVPROX and the first heart sound S1. The processors set an atrial-ventricular pacing (AV) delay based on the IACI-LVPROX and the ΔS1_C. The processors deliver a pacing therapy based on the AV delay.