Patients with autoimmune diseases such as systemic lupus erythematosus (SLE) or antiphospholipid syndrome (APS) are at a higher risk for adverse cardiovascular events associated with increased morbidity and mortality. The increased risk of these events is often associated with rheumatic heart disease (heart valve or mural endocardium damage from rheumatic fever) following microbial infection (i.e., untreated or under-treated streptococcal infection). In particular, the weakening of cardiac vasculature due to rheumatic heart disease makes such patients with autoimmune diseases more susceptible to endocarditis. Endocarditis can be caused by an infection (infective endocarditis) or inflammation tied to disease activity (non-bacterial thrombotic endocarditis [NBTE]). Infective endocarditis among patients with autoimmune diseases may result from exposure to pathogens during dental or surgical procedures. NBTE commonly occurs as a result of fibrin and platelet aggregation on the cardiac valves without bacterial infection. While diagnosis and management can vary based on underlying etiology, an interdisciplinary approach that includes prevention and management from dentists, cardiologists, rheumatologists, and primary care physicians is needed. In addition, increasing patient and physician education on risk factors and prevention strategies is much needed. This manuscript will review the pathophysiology of endocarditis, the association between SLE and APS and endocarditis risk, the diagnosis and management of these autoimmune diseases with a focus on the prevention of cardiovascular disease risk, and make recommendations for diagnostic and management approaches to improve care.