Background Analysis of the effect of COVID-19 on the complete hospital population in England has been lacking. Our aim was to provide a comprehensive account of all hospitalised patients with COVID-19 in England during the early phase of the pandemic and to identify the factors that influenced mortality as the pandemic evolved. Methods This was a retrospective exploratory analysis using the Hospital Episode Statistics administrative dataset. All patients aged 18 years or older in England who completed a hospital stay (were discharged alive or died) between March 1 and May 31, 2020, and had a diagnosis of COVID-19 on admission or during their stay were included. In-hospital death was the primary outcome of interest. Multilevel logistic regression was used to model the relationship between death and several covariates: age, sex, deprivation (Index of Multiple Deprivation), ethnicity, frailty (Hospital Frailty Risk Score), presence of comorbidities (Charlson Comorbidity Index items), and date of discharge (whether alive or deceased). Findings 91 541 adult patients with COVID-19 were discharged during the study period, among which 28 200 (30•8%) in-hospital deaths occurred. The final multilevel logistic regression model accounted for age, deprivation score, and date of discharge as continuous variables, and sex, ethnicity, and Charlson Comorbidity Index items as categorical variables. In this model, significant predictors of in-hospital death included older age (modelled using restricted cubic splines), male sex (1•457 [1•408-1•509]), greater deprivation (1•002 [1•001-1•003]), Asian (1•211 [1•128-1•299]) or mixed ethnicity (1•317 [1•080-1•605]; vs White ethnicity), and most of the assessed comorbidities, including moderate or severe liver disease (5•433 [4•618-6•392]). Later date of discharge was associated with a lower odds of death (0•977 [0•976-0•978]); adjusted in-hospital mortality improved significantly in a broadly linear fashion, from 52•2% in the first week of March to 16•8% in the last week of May. Interpretation Reductions in the adjusted probability of in-hospital mortality for COVID-19 patients over time might reflect the impact of changes in hospital strategy and clinical processes. The reasons for the observed improvements in mortality should be thoroughly investigated to inform the response to future outbreaks. The higher mortality rate reported for certain ethnic minority groups in community-based studies compared with our hospital-based analysis might partly reflect differential infection rates in those at greatest risk, propensity to become severely ill once infected, and health-seeking behaviours.