The aim of this study was to evaluate differences in the clinical manifestations and outcomes in hospitalized patients with COVID-19 in a single Romanian center during four pandemic waves determined by different SARS-CoV-2 variants of concern (VOCs). A retrospective study on 9049 consecutive hospitalized adult patients was performed between 27 February 2020 and 31 March 2023. The study interval was divided into waves based on national data on SARS-CoV-2 VOCs’ circulation. Multivariate logistic regression models were built, predicting death and complications as functions of comorbidities, therapy, wave, severity form, and vaccination status, and adjusted for ages ≥65 years. Pulmonary (pneumothorax/pneumomediastinum, pulmonary embolism) and extrapulmonary complications (liver injury, acute kidney injury, ischemic/hemorrhagic stroke, myocardial infarction, and gastrointestinal bleeding) were present, more frequently in ICU hospitalized patients and with differences between waves. The highest in-hospital mortality was found in patients presenting pneumothorax/pneumomediastinum. All of the evaluated risk factors were significantly associated with death, except for obesity and the Omicron wave. Our study highlights the changing nature of COVID-19 and acknowledges the impacts of viral mutations on disease outcomes. For all four waves, COVID-19 was a severe disease with a high risk of poor outcomes.