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We present the case of an oncology patient admitted to our hospital during the current COVID-19 pandemic with clinical and radiological features strongly suggestive of interstitial pneumonia. Multiple laboratory tests were negative for SARS-CoV-2 (polymerase chain reaction testing of nasopharyngeal swabs, and of induced sputum and stool samples, investigation of serum immunoglobulins G and M). In the setting of an immunocompromised status due to recent chemotherapy cycles for lung adenocarcinoma and prolonged corticosteroid therapy (due to frequent exacerbations of chronic obstructive pulmonary disease in recent months), we actively searched for the pathological agent and found it to be Pneumocystis jirovecii. The patient started specific antibiotic treatment but finally had a negative outcome due to the progression of the lung adenocarcinoma. The importance of differential diagnostics in clinical practice should be a given, especially during times of pandemic. The novel coronavirus infection introduced new guidelines for and approaches to the investigation of immunocompromised patients, so it is especially important not to forget the basis of differential diagnosis, to and adopt a thorough approach when assessing these complex patients. We want to stress the importance of thorough investigation to avoid misdiagnosis of atypical pathogens in the current setting of SARS-CoV-2 pandemic.