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Staphylococcus lugdunensis is a highly virulent coagulase-negative staphylococcus, capable of causing rapidly destructive infective endocarditis (IE). We report an elderly male who developed P wave asystole as the initial manifestation of S. lugdunensis IE, occurring in the absence of fever or classical IE symptoms. Transoesophageal echocardiography (TOE) revealed severe aortic regurgitation from cusp destruction, a perivalvular abscess and an acquired Gerbode defect—a rare left ventricular-to-right atrial communication. An urgent aortic valve replacement was performed, and intraoperatively, the Gerbode defect was found to have spontaneously closed. Due to permanent pacing requirements and infection risk, a leadless pacemaker was implanted. This case underscores the importance of suspecting IE in unexplained conduction abnormalities, recognising the virulence of S. lugdunensis and using early TOE to detect life-threatening structural complications.