Background <p>Isavuconazole (ISA), voriconazole (VCZ), and amphotericin B and its derivatives (AMB) are broad-spectrum antifungal drugs. However, there is no comparison of the effectiveness and safety of ISA, AMB, and VCZ in invasive mold disease (IMD).</p> Methods <p>We conducted a real-world retrospective single-center observational cohort study of patients with proven or probable IMD who received ISA, AMB formulations, or VCZ. The primary outcome was 42-day all-cause mortality; secondary outcomes included 84-day all-cause mortality, in-hospital clinical response, and treatment-related adverse events.</p> Results <p>A total of 299 patients were included: 40 in the ISA group, 33 in the AMB group, and 226 in the VCZ group. Crude 42-day mortality was 5.0%, 24.2%, and 12.8%, respectively, and crude 84-day mortality was 7.5%, 36.4%, and 17.3%, respectively. After adjustment for major baseline and pathogen imbalances, ISA was associated with lower 42-day mortality than VCZ (adjusted OR 0.07 (95% CI 0.01–0.62), <i>p</i> = 0.017) and lower 84-day mortality (adjusted HR 0.18 (95% CI 0.04–0.75), <i>p</i> = 0.019), whereas AMB was not significantly different from VCZ. ISA was also associated with lower rates of renal and hepatic adverse events than AMB formulations.</p> Conclusions <p>In this retrospective cohort, ISA was associated with lower adjusted mortality than VCZ. ISA associated with favorable clinical outcomes and an acceptable safety profile in real-world IMD practice.</p> Trial registration <p>Clinical trial number: not applicable.</p>