Background The need for new permanent pacemaker implantation (PPI) after Transcatheter Aortic Valve Implantation (TAVI) remains a critical issue. Membranous Septum (MS) length is associated with PPI after TAVI. The aim of this study was to identify different MS thresholds for the contemporary THV-platforms. Methods This retrospective, case-control study enrolled all patients who underwent a successful TAVI procedure with contemporary THV-platforms in the Erasmus University Medical Center between January 2016 and March 2020. The follow-up period for new PPI was 30 days. MS-length was determined by Computed Tomography. Results The study consisted 653 TAVI patients with median age 80.6 years (IQR 74.7–84.8). New PPI occurred in 120 patients (18.4%). Patients with new PPI had a shorter MS-length (2.9 mm (IQR 2.3–4.3) vs. 4.2 mm (IQR 2.9–5.7), p < 0.001). MS-length < 3 mm identified a high-risk phenotype with 30.3% PPI-rate (OR 6.5 [95%CI 2.9–14.9]), MS-length 3–6 mm an intermediate-risk phenotype with 15.4% PPI-rate (OR 2.7 [95%CI 1.2–6.2]) and MS > 6 mm a low-risk phenotype with a 6.3% PPI-rate (reference). For the Lotus valve, there was no significant difference in PPI-rates between the high-risk (45.8%, OR 3.5 [95%CI 0.8–15.1]) and low-risk group (20%). By multivariate analysis MS-length, Agatston-score, use of Lotus valve, and ECG with first-degree AV block, RBBB or bifascular block were independent predictors for new PPI. Conclusion MS-length was an independent predictor for new PPI post-TAVI. Three phenotypes were found based on MS-length. MS < 3 mm was universally associated with a high risk for new PPI (>30%). MS > 6 mm represented a low-risk phenotype with PPI-rate < 10%. PPI-rate varied per THV type in the intermediate phenotype. PPI-rate with Lotus was high regardless of MS-length.