BACKGROUND: Many respiratory pathogens have been identified in people living with HIV-1 and pulmonary infection, but their impact on clinical outcomes remains largely unclear. METHODS: Metagenomic sequencing and traditional laboratory diagnostics were applied to identify bacterial, viral, and fungal respiratory pathogens. Clinical outcomes were assessed by (i) mortality or ICU transfer during hospitalization, and (ii) 30-day re-hospitalization and 180-day mortality after hospital discharge. RESULTS: Microbiological analyses of bacterial, viral and fungal pathogens in 237 in-patients with HIV-1 and pulmonary infections revealed Pneumocystis jirovecii (58 %) as the most prevalent respiratory pathogen, followed by Cytomegalovirus (39 %), Mycobacterium tuberculosis (22 %), Talaromyces marneffei (17 %), and Epstein-Barr virus (16 %). Fifty-six patients (24 %) were coinfected with bacterial, viral and fungal pathogens, referred to as bacterial+fungal+viral coinfections. Risk factors for bacterial+fungal+viral coinfections (RR=8.41, 95 %CI: 4.2-14.3), severe pneumonia (RR=13.6, 95 %CI: 8.14-19.3), and elevated C-reactive protein levels (RR=6.42, 95 %CI: 1.58-10.13) were significantly associated with mortality or ICU transfer during hospitalization. After hospital discharge, 38 patients (16 %) were rehospitalized within 30 days. Antiretroviral therapy reduced the risk of 30-day rehospitalization (HR=0.21, p = 0.01). During the 180-day follow-up, 13 patients (5.5 %) died. Survival analyses identified severe pneumonia and age ≥ 60 years as risk factors for 180-day mortality. CONCLUSIONS: Multiple pulmonary coinfections are associated with severe outcomes in in-patients with HIV-1 infection. Effective management of both HIV-1 and pulmonary infections is crucial to reduce hospitalization rates and mortality risk.