Introduction Influenza is a major concern in hospitals, including the emergency department (ED), mainly because of a high risk for ED personnel to acquire and transmit the disease. Although influenza vaccination is recommended for health care workers, vaccination coverage is low. Methods This survey was conducted in the 2016/2017 and 2020/2021 influenza seasons. Questionnaires were sent to ED personnel in 12 hospitals in Bavaria, South-Eastern Germany. The response rates were 62% and 38% in 2016/2017 and 2020/2021, respectively. Data were compared between the two seasons as well as between vaccinated and not vaccinated respondents in 2020/2021. Results Significantly more ED personnel reported having been vaccinated in the 2020/2021 season. Factors associated with vaccination coverage (or the intention to get vaccinated) were profession (physician / medical student), having been vaccinated at least twice, the availability of an influenza vaccination on site (in the ED) as well as the COVID-19 pandemic. Additionally, significant differences in the assessment and evaluation of influenza, its vaccination side effects and ethical aspects were found between vaccinated and not vaccinated ED personnel in 2020/2021. Unvaccinated respondents estimated higher frequencies of almost all potential vaccination side effects, were less likely to accept lay-offs if employees would not come to work during an influenza pandemic and more likely to agree that work attendance should be an employees decision. Vaccinated participants instead, rather agreed that vaccination should be mandatory and were less likely to consider job changes in case of a mandatory vaccination policy. Conclusion The COVID-19 pandemic might have contributed to a higher influenza vaccination rate among ED workers. Vaccination on site and interventions targeting the perception of influenza vaccination and its side effects may be most promising to increase the vaccination coverage among ED personnel.