Abstract Aims No studies have compared Watchman 2.5 (W2.5) with Watchman FLX (FLX) devices to date. We aimed at comparing the FLX with W2.5 devices with respect to clinical outcomes, left atrial appendage (LAA) sealing properties and device-related thrombus (DRT). Methods and results All consecutive left atrial appendage closure (LAAC) procedures performed at two European centres between November 2017 and February 2021 were included. Procedure-related complications and net adverse cardiovascular events (NACE) at 6 months after LAAC were recorded. At 45-day computed tomography (CT) follow-up, intra- (IDL) and peri- (PDL) device leak, residual patent neck area (RPNA), and DRT were assessed by a Corelab. Out of 144 LAAC consecutive procedures, 71 and 73 interventions were performed using W2.5 and FLX devices, respectively. There were no differences in terms of procedure-related complications (4.2% vs. 2.7%, P = 0.626). At 45-day CT, the FLX was associated with lower frequency of IDL [21.3% vs. 40.0%; P = 0.032; odds ratio (OR): 0.375; 95% confidence interval (CI): 0.160–0.876; P = 0.024], similar rate of PDL (29.5% vs. 42.0%; P = 0.170), and smaller RPNA [6 (0–36) vs. 40 (6–115) mm2; P = 0.001; OR: 0.240; 95% CI: 0.100–0.577; P = 0.001] compared with the W2.5 group. At 45 days, rate of DRT as detected by CT and/or transoesophageal echocardiography (TOE), was higher with W2.5 (6.0% vs. 0%, P = 0.045). At 6-month follow-up, NACE did not differ between groups. Conclusions In this cohort of consecutive LAACs, FLX as compared to W2.5, was associated with similar procedure-related complications and 6-month NACE, but with improved LAA neck coverage, and lower IDL and DRT.