Understanding public risk perception is an essential step to develop effective measures reducing the spread of disease outbreaks. Here we compare epidemic risk perceptions during two different periods of the COVID-19 pandemic in Italy and Sweden. To this end, we analyzed the results of two nationwide surveys carried out in both countries in two periods characterized by different infection rates: August (N = 4154) and November 2020 (N = 4168). Seven domains of epidemic risk perception were considered: likelihood along with (individual and population) impact, preparedness, and knowledge. The role of the context and period was explored in stratified and formal interaction analyses. In both countries, we found an intensification in epidemic risk perception from August to November 2020. Being male, older and having a higher relative income were associated with a lower perception of the likelihood of epidemics, while excess mortality was marginally related to higher odds. Compared to Sweden, Italy had a higher increase in perception of likelihood and impact, and a concurrent decrease in preparedness and knowledge. The different authority response to the COVID-19 pandemic is associated with a different change over time in risk perception. Regional differences in terms of excess mortality only marginally explained differences in risk perception.