Purpose: To reconstruct whole-heart images from free-running acquisitions through automated selection of data acceptance windows (ES: end-systole, MD: mid-diastole, ED: end-diastole) that account for heart rate variability (HRV). Methods: SYMPHONIC was developed and validated in simulated (N = 1000) and volunteer (N = 14) data. To validate SYMPHONIC, the position of the detected acceptance windows, total duration, and resulting ventricular volume were compared to the simulated ground truth to establish metrics for temporal error, quiescent interval duration, and volumetric error, respectively. SYMPHONIC MD images and those using manually defined acceptance windows with fixed (MANUALFIXED) or adaptive (MANUALADAPT) width were compared by measuring vessel sharpness (VS). The impact of HRV was assessed in patients (N = 6). Results: Mean temporal error was larger for MD than for ED and ED in both simulations and volunteers. Mean volumetric errors were comparable. Interval duration differed for ES (p = 0.04) and ED (p < 10–3), but not for MD (p = 0.08). In simulations, SYMPHONIC and MANUALADAPT provided consistent VS for increasing HRV, while VS decreased for MANUALFIXED. In volunteers, VS differed between MANUALADAPT and MANUALFIXED (p < 0.01), but not between SYMPHONIC and MANUALADAPT (p = 0.03) or MANUALFIXED (p = 0.42). Conclusion: SYMPHONIC accurately detected quiescent cardiac phases in free-running data and resulted in high-quality whole-heart images despite the presence of HRV.