Over the past 30 years, there has been an increasing number of documented human infections associated with the protozoan Lophomonas, specifically Lophomonas blattarum, which is considered a relatively rare infection. These infections are primarily associated with states of immune suppression, including those resulting from corticosteroid therapy. We report a 61-year-old female patient with a 20-year medical history of Systemic lupus erythematosus (SLE) who was admitted due to persistent respiratory symptoms that were unresponsive to treatment. The patient was receiving immunosuppressive therapy for SLE. Upon hospitalization, computed tomography of the lungs revealed the presence of centrilobular nodules exhibiting tree-in-bud patterns, as well as bronchiectasis, predominantly in the middle and lower lobes. Subsequently, the patient underwent bronchoscopy, during which a BAL sample was obtained. Microscopic analysis of the sample indicated the presence of L. blattarum. Clinicians often focus on the primary symptoms of SLE, but they must also consider the risk of severe respiratory complications like lophomoniasis. This condition is critical to address in the management of SLE patients, who are immunosuppressed due to the disease's nature and its treatment.