•Mycobacterium marinum disseminated infections occur rarely in immunocompromised patients.•Treatment of M. marinum infections requires a prolonged multi-drug regimen.•Side effects and drug–drug interaction are frequent with a concomitant regimen.•Bedaquiline may be an alternative treatment for M. marinum infections. Disseminated Mycobacterium marinum infections occur rarely, in immunocompromised patients. Treatment with a prolonged multi-drug regimen exposes patients to drug–drug interactions and side effects. We report a case of disseminated M. marinum infection in a 54-year-old renal transplant, HIV-infected woman. Manifestations of the infection were cutaneous and subcutaneous nodules, mediastinal lymph nodes and left pulmonary infiltrate. Empirical treatment for non-tuberculous mycobacteria was initiated with rifabutin, ethambutol and azithromycin. After identifying M. marinum in sputum, due to unfavourable clinical evolution and severe drug-related adverse events, treatment was changed to doxycycline and rifabutin. Digestive and haematologic side effects motivated a change in antimycobacterial treatment to a combination of moxifloxacin and bedaquiline. Tolerance was satisfactory, and the patient was cured after 12 months of treatment. We report (to the authors’ knowledge) the first case of disseminated M. marinum infection successfully treated with a bedaquiline-containing regimen. Bedaquiline could be an alternative to recommended antimicrobial regimens in cases of non-tuberculous mycobacterial disease, including M. marinum infection.