Pneumonia due to Mycobacterium malmoense is rare and usually occurs in damaged lung as is the case with Aspergillus infections. We report the case of a patient who developed chronic necrotizing pulmonary aspergillosis following an infection by atypical mycobacteria. A 53-year-old woman was hospitalized because of weight loss and fever. Direct examination of sputum smear was positive for acid fast bacilli and PCR and culture led to the diagnosis of infection with M. malmoense. Treatment was begun with clarithromycin, rifampicin and ethambutol. Despite initial improvement and excellent adherence to treatment, fever and weight loss recurred 6 months later. Relapse of the mycobacterial infection was excluded and the final diagnosis was necrotizing pulmonary aspergillosis. Infection with A. fumigatus complicating the treatment of M. malmoense is unusual. The management is challenging because of strong interactions between voriconazole and rifampicin, and thus requires a multidisciplinary and specialized approach.