Objectives: To assess and compare influenza and COVID-19 vaccination uptake of Swiss healthcare workers (HCWs) in primary care 2020/21. Methods: Influenza and COVID-19 vaccination uptake and recommendation behaviours of HCWs in the primary care were assessed using an online semi-structured questionnaire. Associations between vaccination rates and age, language, gender, profession, vaccination history, vaccination training and recommendation behaviours were evaluated using descriptive and multivariable logistic regression analyses. Results: Vaccinated against COVID-19 in 2020/21 were 91.8% of the 1,237 participating HCWs, while 60.1% were vaccinated against influenza. Physicians and pharmacists presented the highest influenza vaccination rates (87.3%, 73.7%, respectively) compared to nurses (45.8%) and medical practice assistants (52.5%) while COVID-19 vaccination rates were high across all professions. Influenza and COVID-19 vaccination rates were significantly associated with age, profession, vaccination history, vaccination training and recommendation behaviours. Conclusion: Acceptance for influenza vaccination has increased during the pandemic but is lower than that for COVID-19 among the HCWs. Demographics, vaccination status and vaccination training impact the vaccination behaviour among HCWs and should be considered in future campaigns to increase vaccination uptake.