Addressing the challenge of vaccine hesitancy is crucial in managing public health crises like the COVID-19 pandemic. This study leverages the U.S. Census Bureau’s Household Pulse Survey to examine COVID-19 vaccine hesitancy, with a specific focus on the longitudinal tracking of vaccination beliefs and the influence of varying risk perceptions. It investigates how public attitudes towards vaccines evolve, influenced by changing perceptions of COVID-19 risk and vaccine safety. By applying Secondary Risk Theory (SRT), the research elucidates the relationship between different risk perceptions and vaccine hesitancy. We find that threat perception of COVID-19 and lack of trust in the vaccine demonstrate strong predictive value of increased vaccine hesitancy in comparison to other reasons for hesitancy such as access to vaccines, vaccine efficacy beliefs, or perceived secondary risks about vaccine side effects. Respondents with very low primary threat beliefs that COVID-19 is not a threat were 5.65 times more likely (β = 1.732) to intend not to be vaccinated in January 2021, decreasing to 2.70 times more likely to avoid vaccination (β = 0.995) in the December 2021.