Abstract Background Pulsed field ablation (PFA) offers a safe, non-thermal alternative for pulmonary vein isolation (PVI) in patients with atrial fibrillation (AF). Currently, the pentaspline PFA-system relies heavily on fluoroscopy for catheter manipulation, which poses challenges due to the complexity of left atrium anatomy. Incorporating three-dimensional electroanatomical mapping (3D-EAM) could improve procedural efficiency reducing dependency on fluoroscopy guidance. This study aims to evaluate the effects of integration of 3D-EAM with PFA during PVI. Methods Between September 2022 and December 2023, we retrospectively enrolled 248 patients with paroxysmal or persistent AF undergoing PVI at our center using the pentaspline PFA catheter. The control group (n = 104) received conventional PFA with fluoroscopic guidance alone, while the intervention group (n = 144) underwent PVI with PFA with 3D-EAM integration. Primary outcomes were procedural time, fluoroscopy time (FT), and dose area product (DAP). Secondary endpoints included acute procedural success and incidence of periprocedural complications. Results In the 3D-EAM-PFA group, procedural time was 63.3 ± 14.3 min, compared to 65.6 ± 14.9 min in the control group (p = 0.22). The 3D-EAM group experienced significantly reduced FT (9.7 ± 4.4 min vs. 16.7 ± 5.2 min) and DAP (119.2 ± 121.7 cGycm2 vs. 338.7 ± 229.9 cGycm2) compared to the control group, respectively (p < 0.001). Acute procedural success was achieved in all cases. No major complications were observed in either group. Conclusion Integration of 3D-EAM with the pentaspline PFA catheter for PVI in AF treatment offers a promising approach, with significantly reduced fluoroscopy exposure without compromising procedural time and efficacy. Graphical abstract