Congenital heart disease (CHD) remains a predisposing cardiac condition for infective endocarditis (IE). Case report: We present the case of 8-year-old boy with no known pre-existing cardiac disease diagnosed with infective endocarditis (IE) with Gemella sanguinis. After admission, he underwent transthoracic echocardiography (TTE), which revealed the presence of Shone syndrome with a bicuspid valve, mitral parachute valve and severe aortic coarctation. He developed a paravalvular aortic abscess with severe aortic regurgitation and left ventricle (LV) systolic dysfunction for which he required a complex surgical intervention after six weeks of antibiotic treatment, consisting of Ross operation and coarctectomy, with a complicated postoperative course, cardiac arrest and ECMO support for five days. The evolution was slow and favorable, with no significant residual valvular lesions. However, persistent LV systolic dysfunction and increased muscle enzymes required further investigation to establish a genetic diagnosis of Duchenne disease. As Gemella is not considered a frequent pathogen of IE, no current guidelines refer specifically to it. Additionally, the predisposing cardiac condition of our patient is not currently classified as “high-risk” for IE; this is not considered an indication for IE prophylaxis in the current guidelines. Conclusion: This case illustrates the importance of accurate bacteriological diagnosis in infective endocarditis and poses concerns regarding the necessity of IE prophylaxis in “moderate risk” cardiac conditions such as congenital valvular heart disease, especially aortic valve malformations.