Background Despite developments in the past 20 years in the treatment of native valve (NVE) endocarditis, including the multidisciplinary endocarditis team approach and advances in perioperative care, outcome improvements are lacking. This study compares a contemporary with a historic cohort of NVE patients. Methods All patients undergoing first-time cardiac surgery for NVE in two periods were evaluated in a retrospective observational single-center trial. The historic period included patients from 1998 to 2003 and the contemporary cohort 2021 to 2024. Results Of the 359 patients who were included, 155 were in the historic cohort (years 1998–2003) and 204 in the contemporary (years 2021–2024). The annual caseload increased significantly from 25.8 to 51.0 annual cases (p < 0.01). Patient baselines changed, being nowadays older (62.6 vs. 55.5 years, p < 0.001), having higher BMI (26.9 kg/m ² vs. 25.3 kg/m ², p < 0.01) and higher EuroSCORE II (8.7% vs. 5.0%, p < 0.001). Accordingly, the preoperative clinical presentation also worsened with an increase in septic embolizations (33.8% vs. 22.6%, p ¼ 0.04) and acute kidney injury (15.2% vs. 1.9%, p < 0.001). Minimally invasive procedures were newly established (41.2% vs. 0%). The contemporary group faced a higher rate of postoperative dialysis, longer intensive care unit stay, and higher perioperative mortality (14.2% vs. 6.5%, p ¼ 0.03). Nonetheless, survival at 1 year was comparable (78.4% vs. 79.9, p ¼ 0.52). Conclusion Contemporary patients have higher risk profiles and annual caseloads. This translates into increased postoperative morbidity and mortality; however long-term outcomes have remained constant.