Abstract Background Acute kidney injury (AKI) may develop in coronavirus disease 2019 (COVID-19) patients and may be associated with a worse outcome. The aim of this study is to describe AKI incidence during the first 45 days of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Spain, its reversibility and the association with mortality. Methods This was an observational retrospective case–control study based on patients hospitalized between 1 March and 15 April 2020 with SARS-CoV-2 infection and AKI. Confirmed AKI cases were compared with stable kidney function patients for baseline characteristics, analytical data, treatment and renal outcome. Patients with end-stage kidney disease were excluded. Results AKI incidence was 17.22% among 3182 admitted COVID-19 patients and acute kidney disease (AKD) incidence was 6.82%. The most frequent causes of AKI were prerenal (68.8%) and sepsis (21.9%). Odds ratio (OR) for AKI was increased in patients with pre-existent hypertension OR 2.58, 95% confidence interval (CI) 1.71–3.89 and chronic kidney disease (CKD) (OR 2.14, 95% CI 1.33–3.42) and in those with respiratory distress (OR 2.37, 95% CI 1.52–3.70). Low arterial pressure at admission increased the risk for Stage 3 AKI (OR 1.65, 95% CI 1.09–2.50). Baseline kidney function was not recovered in 45.73% of overall AKI cases and in 52.75% of AKI patients with prior CKD. Mortality was 38.5% compared with 13.4% of the overall sample population. AKI increased mortality risk at any time of hospitalization (hazard ratio 1.45, 95% CI 1.09–1.93). Conclusions AKI is frequent in COVID-19 patients and is associated with mortality, independently of acute respiratory distress syndrome. AKD was also frequent and merits adequate follow-up. Graphical Abstract