Background: Heart failure (HF) and atrial fibrillation (AF) often coexist, but data on the prognostic value of differing ablation strategies according to left ventricular ejection fraction (LVEF) are rare. Methods and results: From January 2007 until January 2010, 728 patients with HF were enrolled in the multi-center German ablation registry prior to AF catheter ablation. Patients were divided into three groups according to LVEF: HF with preserved LVEF (≥ 50%, HFpEF, n = 333), mid-range LVEF (40–49%, HFmrEF, n = 207), and reduced LVEF (< 40%, HFrEF, n = 188). Ablation strategies differed significantly between the three groups with the majority of patients with HFpEF (83.4%) and HFmrEF (78.4%) undergoing circumferential pulmonary vein isolation vs. 48.9% of patients with HFrEF. The latter underwent ablation of the atrioventricular (AV) node in 47.3%. Major complications did not differ between the groups. Kaplan–Meier survival analysis demonstrated a significant mortality increase in patients with HFrEF (6.1% in HFrEF vs. 1.5% in HFmrEF vs. 1.9% in HFpEF, p = 0.009) that was limited to patients undergoing ablation of the AV node. Conclusions: Catheter ablation strategies differ significantly in patients with HFpEF, HFmrEF, and HFrEF. In almost 50% of patients with HFrEF AV-node ablation was performed, going along with a significant increase in mortality rate. These results should raise efforts to further evaluate the prognostic effect of ablation strategies in HF patients.