Abstract Background Eastern Europe witnessed substantial life expectancy losses in 2021. COVID-19 vaccination coverage was lower, and mortality was higher than in Western Europe. Research suggests an important factor behind lower vaccination coverage is vaccine hesitancy. Our studies aimed to explore spatial inequalities in COVID-19 morbidity, mortality, and vaccination coverage in Hungary and the reasons behind vaccine hesitancy during the 3rd and 4th pandemic waves. Methods We characterized COVID-19 morbidity, mortality, and vaccination coverage by indirectly standardized ratios at the municipality level and investigated the association with deprivation. Attitudes towards vaccination were measured by a nationally representative monthly questionnaire survey. Results In Hungary, people in the most deprived municipalities had 17-58% higher relative COVID-19 mortality than the national average, although morbidity was significantly lower. COVID-19 vaccination coverage among the least deprived was 9.2% (95% CI 9-9.5%) higher, while in the most deprived areas, it was 38.2% (95% CI 38.0-38.4%) below the national average at the end of the 3rd pandemic wave. In the 10 districts with the highest proportion of the Roma population, vaccination coverage was 56.0% of the national average (95% CI 55.0-64.0%). Inequalities persisted by the end of the 4th pandemic wave. Younger age, lower education, and lower income were major determinants of vaccine refusal. Reasons for refusal mostly resulted from barriers to accessing reliable information and mistrust. Although Hungary has traditionally had high social acceptance of vaccination, the campaign failed to close the gap in COVID-19 mortality. Hungary demonstrates how social inequalities, misinformation, and mistrust can undermine a vaccination program's success. Consistent, credible communication can dispel misconceptions and build trust, which is key to the acceptance of public health measures.