A 60-year-old male kidney transplant recipient developed fever and bilateral Legionella pneumophila pulmonary nodules 5 months after the procedure, which progressed to cavitary pneumonia despite empiric antifungal and antibacterial therapy. The diagnosis was confirmed by next-generation metagenomic sequencing (mNGS) in bronchoalveolar lavage fluid, which revealed high levels of L. pneumophila. Initial treatment with azithromycin brought temporary improvement, but the condition on x-rays worsened. Prolonged combined treatment with azithromycin and levofloxacin resulted in rapid relief of symptoms, resolution of the cavity on computed tomography, and preservation of function of the transplanted kidney. Sequential blood mNGS showed decreasing pathogen values in parallel with recovery. This first Asian case highlights that mNGS shortens the time to diagnosis in inconclusive routine tests, legionellosis can produce atypical cavitary lesions in immunocompromised patients requiring imaging follow-up, and prolonged combination macrolide and fluoroquinolone therapy is required in severe cases.