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Background: Studies suggest vaccine hesitancy is an increasingly significant phenomenon in Brazil and other countries. Moreover, political ideologies have emerged as an influencing factor for vaccine hesitancy during the COVID-19 pandemic. Methods: In this study, we use information from publicly available databases to investigate the association between political alignment, depicted by the percentage of Bolsonaro voters in the presidential elections of 2018 and 2022, and COVID-19 vaccination in Brazilian municipalities, adjusted for human development index (HDI) scores and basic sociodemographic characteristics of voters. Findings: For both the 2018 and 2022 elections, higher percentages of Bolsonaro voters were significantly associated with a lower vaccination index after adjustment for voters' sociodemographic characteristics. We also found a statistically significant interaction between the percentage of Bolsonaro voters and HDI, with a more significantly detrimental effect of the right-wing political stance in municipalities in the lower HDI quartile. Interpretation: Our study highlights what may be the beginning of a new scenario with unforeseen challenges for vaccine programs: the politicization of vaccines. Strategies to face these challenges should include joint efforts from governments and civil society for a common public health goal. Funding: This manuscript received no specific funding