Obesity and diabetes are risk factors for atrial fibrillation (AF) incidence and recurrence after catheter ablation. However, their impact on post-ablation complications in real-world practice is unknown. Using the Nationwide Inpatient Sample (2005–2013), we examine annual trends in AF ablations and outcomes in US patients with obesity and diabetes and perform multivariate analyses to assess whether they are independently associated with adverse outcomes. Our primary outcome included the composite of in-hospital complications or death. Annual trends for primary outcome, length-of-stay (LOS) and total inflation-adjusted hospital charges were examined. An estimated 106,462 AF-ablations were performed in the US from 2005–2013. There was a gradual annual increase in ablations performed in obese and diabetic patients and complication rates. The primary outcome rate was 11.7% in obese vs. 8.2% in non-obese and 10.7% in diabetic vs. 8.2% in non-diabetic patients (p < 0.001). Obesity was independently associated with increased complications (adjusted-OR, 95% CI:1.39, 1.20–1.62), longer LOS (1.36, 1.23–1.49), and higher charges (1.16, 1.12–1.19). Diabetes was only associated with longer LOS (1.27, 1.16–1.38). Hence obesity, but not diabetes, is an independent risk factor for immediate post AF ablation complications and higher costs. Future studies should investigate whether weight loss prior to ablation reduces complications and costs.