Background The SARS-CoV-2 virus caused the global COVID-19 pandemic, with waxing and waning course. This study was conducted to compare outcomes in the first two waves, in mechanically ventilated patients. Methods This retrospective observational study included all mechanically ventilated COVID-19 patients above 18 years of age, between March 2020 and January 2021. Patients were grouped into first wave from March 2020 to July 2020, and second wave from August 2020 to January 2021. Outcome measures were mortality, the development of acute kidney injury (AKI), and need for renal replacement therapy (RRT). Univariate and multivariate cox regression analysis were used to delineate risk factors for the outcome measures. Results A total of 426 patients, 285 in the first wave and 185 in the second wave, were included. The incidence of AKI was significantly lower in the second wave (72% vs. 63%; p=0.04). There was no significant difference in mortality (70% vs. 63%; p=0.16) and need for RRT (36% vs. 30%; p=0.1). Risk factors for mortality were increasing age and AKI in both waves, and chronic kidney disease (CKD) (adj. HR 1.7; 95% CI 1.02–2.68; p=0.04) in the second wave. Risk factors for AKI were CKD in both the waves, while it was diabetes (adj. HR 1.4; 95% CI 1.02–1.95; p=0.04) and increasing age in the first wave. Remdesivir (adj. HR 0.5; 95% CI 0.3–0.7; p < 0.01) decreased the risk of AKI, and convalescent plasma (adj. HR 0.5; 95% CI 0.3–0.9; p=0.02) decreased the risk of mortality in the first wave, however, such benefit was not observed in the second wave. Conclusions Our study shows a decrease in the incidence of AKI in critically ill patients, however, the reason for this decrease is still unknown. Studies comparing the waves of the pandemic would not only help in understanding disease evolution but also to develop tailored management strategies.