To compare the morbidity and work absenteeism associated with coronavirus disease 2019 (COVID-19) and influenza among healthcare personnel (HCP) in 2022-2023. We followed 5752 hospital-based HCP in Greece from November 14, 2022 through May 28, 2023. Symptomatic HCP were tested for SARS-CoV-2 and influenza by real-time PCR and/or rapid antigen detection test. The association between the duration of absenteeism and the type of disease was estimated by multivariable regression models. A total of 734 COVID-19 cases and 93 influenza cases were studied. The mean duration of absence per COVID-19 case was 5.8 days compared with a mean of absence of 3.6 days per influenza case (p-value <0.001). Overall, COVID-19 accounted for 4245 days missed during the study period compared with 333 days missed due to influenza. Multivariable regressions estimates indicated that HCP with COVID-19 had 1.91 more days of absenteeism [95% confidence interval (CI): 1.67 to 2.15] compared to those with influenza, on average. As SARS-CoV-2 becomes endemic, COVID-19 remains the prevalent cause of morbidity and absenteeism among HCP, accounting for considerably more workdays missed compared with influenza. HCP should be up-to-date with COVID-19 booster vaccinations and annual influenza vaccination in order to protect them as well as healthcare systems from HCP absenteeism.