Influenza is a health problem and vaccination is the most effective measure to prevent it. The objective of this study was to evaluate the impact of the COVID-19 pandemic on vaccination coverage (VC) against influenza in healthcare workers (HCWs). A cross-sectional study was conducted at the Dr. Balmis University General Hospital in the province of Alicante (Spain), in which vaccination data were collected retrospectively. Adverse effects (AEs) were detected via telephone call between 15 and 30 days after vaccination. The existence of significant changes in VC between the different seasons studied was evaluated using Chi square with a statistical significance level of p < 0.05. A total of 8403 HCWs vaccinated throughout the different seasons were studied. The vaccination coverage of HCWs for influenza pre-COVID-19 pandemic (2019/20 season) was 51.9%; increased during the pandemic to 67.9% (2020/21 season) and 65.5% (2021/22 season); and, after the pandemic, it decreased to 42.7% (2022/23 season) (p < 0.05). The most frequent reason for vaccination during the periods evaluated was “self-protection”, followed by “protection of patients” and “protection of family members”. Of all HCWs evaluated, 26.6% (1460/5493) reported at least one AE. During the COVID-19 pandemic, HCWs’ influenza vaccination coverage fluctuated considerably. There has been an increase in VC during the most critical moments of the pandemic, both in the 2020/21 and 2021/22 seasons, which has, subsequently, decreased in the 2022/2023 season, to levels below pre-pandemic (2019/2020 season), which justifies implementing specific measures to recover VC in Spain.