We report a patient with COVID-19 requiring hospitalization for two weeks, complicated by multiple segmental pulmonary embolisms for which dabigatran was initiated. After clearing the infection, the patient remained asymptomatic for 5 months. He was then readmitted with a spontaneous haemothorax, most likely related to the use of dabigatran, which progressed to a pleural empyema with a trapped lung. The patient underwent a video assisted thoracoscopy (VATS) with decortication. Because of focal abnormalities, biopsies for histopathology were taken from the lung parenchyma. These showed an organizing pneumonia with progression towards fibrosis and arteries with intimal fibrosis. So far, no histopathological reports exist on late pulmonary changes after a COVID-19 infection. The unusual combined presence of microvascular damage and interstitial fibrosis may reflect a pathophysiological concept in which early endothelial damage by SARS-CoV-2 can lead to a chronic state of microvascular damage, low grade inflammation, and early progression towards pulmonary fibrosis.