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Patients with chronic diseases, such as Chronic Obstructive Pulmonary Disease (COPD) and diabetes mellitus, are exposed to particular complications that require a careful diagnostic algorithm. Pulmonary Embolism (PE) in COPD patients often demands an accurate differential diagnosis and a prompt therapeutic intervention. Aspergillus spp. infection comprises a large spectrum of pathological manifestations, depending on immune status and the presence of underlying lung disease. These manifestations may range from invasive pulmonary aspergillosis (IPA) in gravely immunocompromised patients, to chronic necrotizing aspergillosis (CNA) in patients with chronic lung diseases and moderately compromised immune systems. Aspergilloma is generally observed in patients with cavitary lung diseases, and allergic bronchopulmonary aspergillosis (ABPA) is reported in patients with hypersensitivity to Aspergillus antigens. We report a case with pulmonary aspergillosis arisen on a pulmonary infarction after PE in a patient with COPD and diabetes mellitus. To date, report with this clinical evolution was not reported in literature. This report is intended to describe an accurate diagnostic path in a complex overlap of different pathological conditions, highlighting the great importance of differential diagnosis and an appropriate diagnostic algorithm. In addition, open issues on the real diagnostic value of clinical, radiological, and laboratory features for COPD exacerbation, PE and aspergillosis have been discussed.