Abstract Aims There is limited evidence on the prognostic significance of atrial fibrillation (AF) in patients with low flow, low-gradient aortic stenosis with preserved ejection fraction (LFLG-pEF AS). We aimed to evaluate the recovery of stroke volume after transcatheter aortic valve implantation (TAVI) and clinical outcomes in patients with LFLG-pEF AS stratified by presence or absence of AF. Methods and results In a prospective TAVI registry, patients with preserved left ventricular ejection fraction (LVEF ≥ 50%) were stratified according to flow-gradient status and presence of AF. Among 2259 TAVI patients with preserved LVEF between August 2007 and June 2021, 765 had high-gradient AS (HG AS) and 444 had LFLG-pEF AS. AF was observed in 199 patients with HG AS (26.0%) and 190 patients with LFLG-pEF AS (42.8%). At 1 year, stroke volume index (SVi) was significantly improved in LFLG-pEF AS patients without AF, while SVi remained low in patients with AF (from 25.9 ± 8.5 mL/m2 to 37.2 ± 9.9 mL/m2 and from 26.8 ± 5.1 mL/m2 to 26.1 ± 9.1 mL/m2, respectively). LFLG-pEF AS patients with AF had an increased risk of 1-year all-cause mortality compared with those without AF (adjusted hazard ratio (HRadjusted) 2.57; 95% confidence interval [CI] 1.44–4.59). LFLG-pEF AS patients without AF had similar mortality compared with HG AS patients without AF (HRadjusted 0.85; 95% CI 0.49–1.46). Conclusion Patients with LFLG-pEF AS and AF experienced no relevant recovery of stroke volume after TAVI, but a more than two-fold increased risk of death compared to patients with HG AS or LFLG-pEF AS without AF. Clinical Trial Registration https://www.clinicaltrials.gov. NCT01368250.