The paper aims to detect the differences in stock market performance between companies from the alternative energy sector and main stock market sectors in the first and second years of the COVID-19 pandemic. We used Global Industry Classification Standard to analyse eleven main stock market sectors and the alternative energy sector. Based on the one-factor variance analysis—ANOVA, we reveal the statistically significant differences between the analysed stock market sectors in both 2020 and 2021. The analysis implied that the performance of stock market companies during COVID-19 is sector-specific. Tukey’s Honestly Significant Difference (HSD) test for pairwise comparison indicates that the alternative energy sector shows the most differentiation. Its average rate of return in 2020 is the highest and is significantly different for all eleven stock market sectors, while the top constituents from the conventional energy and financial sectors suffered the most. In 2021, a reverse trend in the stock prices can be observed. Companies from the conventional energy and financial sectors achieved the highest positive average weekly rates of return among all of the analysed stock market sectors, while the alternative energy sector performed significantly worse than the other sectors did. Nevertheless, throughout the entire analyses period of 2020–2021, the companies from the alternative energy sector turned out to be the biggest stock market beneficiaries. This study might imply that the COVID-19 pandemic has not hampered but has instead accelerated growing concerns about the environment and climate change.