Highly pathogenic coronaviruses, including severe acute respiratory syndrome coronavirus 2 (refs. ) (SARS-CoV-2), Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-1 (ref. ), vary in their transmissibility and pathogenicity. However, infection by all three viruses results in substantial apoptosis in cell culture and in patient tissues, suggesting a potential link between apoptosis and pathogenesis of coronaviruses. Here we show that caspase-6, a cysteine-aspartic protease of the apoptosis cascade, serves as an important host factor for efficient coronavirus replication. We demonstrate that caspase-6 cleaves coronavirus nucleocapsid proteins, generating fragments that serve as interferon antagonists, thus facilitating virus replication. Inhibition of caspase-6 substantially attenuates lung pathology and body weight loss in golden Syrian hamsters infected with SARS-CoV-2 and improves the survival of mice expressing human DPP4 that are infected with mouse-adapted MERS-CoV. Our study reveals how coronaviruses exploit a component of the host apoptosis cascade to facilitate virus replication.