Background: Previous studies have elucidated the relationship between causative organism and outcomes in infective endocarditis, however this relationship has not been studies in United States Veterans. The aim of this manuscript is to evaluate the association between causative organism and short-term and long-term outcomes in United States (US) Veterans with infective endocarditis (IE) requiring surgical management between 2010–2020. Methods: We analyzed 489 patients with surgically treated IE from the Veterans Affairs (VA) Surgical Quality Improvement Program and the VA Informatics and Computing Infrastructure databases. Patients were divided into groups using causative organism identified from blood or intraoperative cultures – Staphylococcus, Streptococcus, Gram-negative rods, Enterococcus, Polymicrobial, and Unknown/Culture Negative. Other identified organisms were excluded from analysis. Cox proportional hazard models were used to calculate risk for stroke/transient ischemic attack (TIA), myocardial infarction (MI), and death based on group. The models were adjusted for covariates using backward elimination. Continuous variables were compared using ANOVA or Kruskal-Wallis H tests, and categorical variables were compared using Chi square tests. Results: Mean follow-up was 4.0 ± 6.3 years. Gram negative rods (GNRs) were associated with greater risk of long-term mortality (adjusted hazard ratios (aHR) 2.15, 95% CI: 1.20–3.86, p = 0.01). Enterococcus was associated with long-term risk of MI (aHR 2.05, 95% CI: 1.07–3.94, p = 0.03). Resistant organisms, such as methicillin-resistant staphylococcus aureus, were associated with long-term risk of MI (aHR 2.51, 95% CI: 1.14–5.45, p = 0.02). Polymicrobial infections were associated with greater risk of perioperative complications, including prolonged mechanical ventilation (48 hrs) (aHR 1.76, 95% CI: 1.05–2.97, p = 0.034), tracheostomy (aHR 5.64, 95% CI: 2.35–13.55, p < 0.001), and prolonged ICU stay (5 days) (aHR 1.39, 95% CI: 1.01–1.91, p = 0.043). Conclusions: In US Veterans, polymicrobial infections had notably worse perioperative outcomes but similar long-term outcomes in comparison to monomicrobial infections. GNR infections were associated with increased long-term mortality. Enterococcus and resistant organisms were associated with increased long-term risk of MI. Polymicrobial infections were associated with greater risk of perioperative complications, including prolonged mechanical ventilation, tracheostomy, and prolonged ICU stay.