Background: The role of dominant frequency (DF) in tracking the efficiency of a stepwise catheter ablation (step-CA) in persistent atrial fibrillation (peAF) remains poorly studied. We hypothesized that the DF time-course during step-CA displays divergent patterns between patients in whom a step-CA successfully restores long-term sinus rhythm (SR) and those with recurrence. Methods: This study involved 40 consecutive patients who underwent a step-CA for peAF (sustained duration 19 ± 11 months). Dominant frequency was computed on electrograms recorded from the right and left atrial appendages (RAA; LAA) and the coronary sinus before and during the step-CA synchronously to the 12-lead ECG. Dominant frequency was defined as the highest peak within the power spectrum. Results: Persistent atrial fibrillation was terminated by a step-CA in 28 patients [left-terminated (LT)], whereas 12 patients remaining in AF after ablation [not left-terminated (NLT)] were cardioverted. Over a mean follow-up of 34 ± 14 months, all NLT patients had a recurrence. Among the 28 LT patients, 20 had a recurrence, while 8 remained in SR throughout follow-up. The RAA and V ₁ DF had the best predictive values of the procedural failure to terminate AF (area under the curve; AUC 0.84, p < 0.05). A decision tree model including a decrease in LAA DF ≥ 6.61% during the first 20 min following pulmonary vein isolation (PVI) and a baseline RAA DF <5.6 Hz predicted long-term SR restoration with a sensitivity of 83% and a specificity of 93% (p < 0.05). Conclusion: This study found that high baseline DF values are predictive of unfavorable ablation outcomes. The reduction of the LAA DF at early ablation steps following PVI is associated with procedural AF termination and long-term SR maintenance.