Background Multiple intra-atrial thrombi are found rarely except in the presence of prosthetic valves, intra-cardiac devices, structural connections like foramen ovale and thrombophilia. Case presentation We reported acute thrombosis formation in right and left atrial appendages of a 66-year old man admitted due to progressive dyspnea since 7 days earlier. He had a history of prior laryngeal Squamous Cell Carcinoma, apical hypertrophic cardiomyopathy (HCM), and atrial fibrillation (AF). Infection with COVID-19 was confirmed thereafter. Cardiac Magnetic Resonance Imaging (CMR) suggested the diagnosis of atrial clot superior to neoplasm. After surgical removal of the thrombi, symptoms as well as imaging features of pneumonia were resolved. Conclusions We should focus on different presentations and complications of systemic inflammation especially in the setting of COVID-19 infection. Although risk factors of thrombosis are present in some of these patients, rapid progression as well as unusual types of involvement may indicate to a new trigger.