Background: Infective endocarditis (IE) is a feared complication after surgical aortic valve replacement (SAVR)/transcatheter aortic valve implantation (TAVI). It is not certain which procedure carries a higher risk. Our aim was to assess the risk of IE after SAVR/TAVI. Methods: We conducted an observational study of a prospective cohort, including patients with TAVI/SAVR, from March 2015 to December 2020. IE was defined according to the modified Duke’s criteria. IE occurring during the first 12 months of the procedure was considered early IE, and an episode occurring after 12 months was considered late IE. The propensity score was designed to include variables previously associated with TAVI/SAVR and IE. An inverse probability of treatment weight was generated. Results: In total, 355 SAVR and 278 TAVI were included. Median follow-up, 38 vs. 41 months, p = 0.550. IE occurred in 5 SAVR (1.41%, 95% CI 0.2–2.6) vs. 13 TAVI (4.65%, 95% CI 2.2–7.2), p = 0.016. TAVI patients had more frequent early IE (3.2% vs. 0.3%, p = 0.006). In the PS analyses, IE risk did not differ: OR 0.65, 95% CI 0.32–1.32. Factors associated with TAVI IE included younger age (74y vs. 83y, p = 0.030), complicated diabetes mellitus (38.5% vs. 6.8%, p = 0.002), COPD (46.2% vs. 16.3%, p = 0.015), advanced heart failure (100% vs. 52.9%, p < 0.001), and peripheral arteriopathy (61.5% vs. 26.7%, p = 0.011). Conclusions: Early IE was higher with TAVI, but in the PS analyses, the risk attributable to each procedure was similar. Studies are needed to identify and optimize the risk factors of IE prior to TAVI.