Previous studies have shown that cardiac microacceleration signals, recorded either cutaneously, or embedded into the tip of an endocardial pacing lead, provide meaningful information to characterize the cardiac mechanical function. This information may be useful to personalize and optimize the cardiac resynchronization therapy, delivered by a biventricular pacemaker, for patients suffering from chronic heart failure (HF). This paper focuses on the improvement of a previously proposed method for the estimation of the systole period from a signal acquired with a cardiac microaccelerometer (SonR sensor, Sorin CRM SAS, France). We propose an optimal algorithm switching approach, to dynamically select the best configuration of the estimation method, as a function of different control variables, such as the signal-to-noise ratio or heart rate. This method was evaluated on a database containing recordings from 31 patients suffering from chronic HF and implanted with a biventricular pacemaker, for which various cardiac pacing configurations were tested. Ultrasound measurements of the systole period were used as a reference and the improved method was compared with the original estimator. A reduction of 11% on the absolute estimation error was obtained for the systole period with the proposed algorithm switching approach.