Atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical practice. Although its mechanisms are incompletely understood, electrophysiological and structural remodeling of the atria seem to play an important role in the arrhythmia transition from paroxysmal to persistent. However, the time course of the atrial remodeling along onward episodes of non-induced paroxysmal AF has not been investigated yet. In this work, a non-invasive method, based on the regularity estimation of AF through sample entropy (SampEn), has been used to assess the organization evolution along onward episodes of paroxysmal AF. Given that AF organization has been associated to the number of existing wavelets wandering throughout the atrial tissue, SampEn could be considered as a concomitant estimator of atrial remodeling. The achieved results, in close agreement with previous findings obtained from invasive recordings, showed a progressive disorganization increase along onward episodes of AF for 63% of the analyzed patients and a stable AF organization degree in the remaining 37%. Additionally, a positive correlation between episode duration and SampEn was also noticed (R = 0.541, p < 0.01). As a consequence, it could be considered that atrial electrophysiological dynamics that occur along onward paroxysmal AF episodes are reflected and can be quantified from ECG recordings through non-invasive organization estimation.