Abstract Background Influenza infections pose significant risks for nursing home (NH) residents. Our aim was to evaluate the impact of the cantonal influenza campaign, and influenza vaccination coverage of residents and healthcare workers (HCWs) on influenza burden in NHs in a context of enhanced infection prevention and control measures (IPC) during the SARS-CoV-2 pandemic. Methods We extracted data from epidemic reports provided by our unit to NHs over two consecutive winter seasons (2021-22 and 2022-23) and used linear regression to assess the impact of resident and HCW vaccination coverage, and participation in the campaign, on residents’ cumulative influenza incidence and mortality. Results Thirty-six NHs reported 155 influenza cases and 21 deaths during the two winter seasons corresponding to 6.2% of infected residents and a case fatality ratio of 13.5%. Median vaccination coverage was 83% for residents, 25.8% for HCWs, while 87% of NHs participated in the campaign. Resident vaccination was significantly associated with a decrease in odds of death (odds ratio (OR) 0.96, 95% confidence interval (CI): 0.93–0.99). There was no significant effect of HCW vaccination coverage on resident infections and deaths. Campaign participation was associated with decreased odds of infection and death among residents (OR: 0.17, 95% CI: 0.06–0.47 and OR: 0.06, 95% CI: 0.02–0.17 respectively). Conclusion Our analysis suggests that in a context of reinforced IPC measures, influenza still represents a significant burden for NH residents. The most effective measures in decreasing resident influenza burden in NHs was participation in the cantonal influenza vaccination campaign and resident vaccination.