Background: Despite advanced diagnosis and treatment, infective endocarditis (IE) is a potentially life-threatening condition. The impact of COVID-19 on the diagnosis and outcome of the surgical treatment of IE is uncertain. The aim of this study was to analyze the incidence, characteristics, and outcomes of surgically treated IE before and after the COVID-19 pandemic. Methods: This study retrospectively analyzed the data of 535 patients who underwent valve surgical procedures for IE between January 2010 and December 2022 in a single cardiac surgery center. Patients were divided into two groups depending on the date of their operation: before (n = 393) and after (n = 142) COVID-19 onset. In order to balance the groups, inverse probability of treatment weighting (IPTW) calculated from the propensity score (PS) was applied. Weighted univariate logistic regressions were reported for outcomes; weights were derived from IPTW. Interrupted time series analysis (ITSA) according to Linden’s method was used to evaluate the changes in the manifestation of IE after 11 March 2020. Results: Patients from the post-COVID-19 cohort (after 11 March 2020) had a greater number of comorbidities such as diabetes (29.6% vs. 16.3% p = 0.001), hypertension (71.1% vs. 59.5% p = 0.015), and preoperative kidney injury requiring dialysis (9.2% vs. 2.5% p = 0.002), but the median additive and logistic EuroSCORE were not statistically different. In the post-COVID-19 group, we observed a greater prevalence of Staphylococcus aureus-related endocarditis (24.5% vs. 15.4% p = 0.026), a consequent reduction in Staphylococcus non aureus-related endocarditis (12.2% vs. 20.1% p = 0.048), and a decrease in aortic valve replacements (43.0% vs. 53.9%), while the number of mitral valve replacements and repair was greater (21.1% vs. 15.0% and 6.3% vs. 4.3%, respectively). No differences were found in the two groups concerning early death, death, or relapse at 1 year after surgery. Data obtained by multivariable analysis identified preoperative renal dysfunction requiring dialysis as the only common risk factor for early mortality via stratifying by time periods in analysis. Conclusions: The incidence of surgically treated IE significantly increases after the COVID-19 pandemic with a higher incidence of mitral valve involvement with respect to the aortic valve. Although a delay in surgical timing occurred during the COVID-19 pandemic, data in terms of mortality and outcomes were largely unaffected.