Background Mitochondrial cardiomyopathies represent an uncommon but clinically relevant cause of heart failure with reduced ejection fraction (HFrEF). Their diagnosis is often challenging due to overlap with idiopathic dilated cardiomyopathy (DCM). The presence of systemic manifestations and maternal inheritance patterns may provide important diagnostic red flags. Case presentation A 49-year-old man with obesity, obstructive sleep apnea, sensorineural deafness, hepatic steatosis, cognitive delay and a family history of sudden cardiac death (mother at age 60) presented with abdominal pain and bilateral leg edema. Laboratory tests revealed elevated NT-proBNP, mild troponin rise, and increased CPK. ECG showed sinus rhythm with left axis deviation, borderline atrioventricular conduction, and nonspecific repolarization abnormalities. Echocardiography demonstrated a dilated left ventricle with severely reduced ejection fraction (15-20%) and biatrial enlargement. Coronary angiography excluded obstructive coronary artery disease. Cardiac magnetic resonance confirmed DCM with severe systolic dysfunction and late gadolinium enhancement. Continuous telemetry detected non sustained ventricular tachycardia. Discussion The combination of systemic features (sensorineural deafness, mild palpebral ptosis, hepatic involvement), elevated CPK, conduction abnormalities, maternal family history and cognitive delay raised suspicion of mitochondrial cardiomyopathy. Genetic testing for DCM-associated genes was negative. An ICD was implanted given severe LV dysfunction, myocardial fibrosis, and ventricular arrhythmias. At one-year follow-up, the patient remained clinically stable, with persistent LV dysfunction but improved symptoms. Importantly, a multidisciplinary evaluation prompted neurological consultation, which recommended a muscle biopsy to further investigate mitochondrial involvement. Conclusion This case underscores the importance of recognizing extracardiac red flags in patients with apparently idiopathic DCM. A multidisciplinary approach, integrating cardiology, genetics, and neurology, is essential to refine diagnosis, with muscle biopsy playing a pivotal role in confirming mitochondrial disease and guiding management.