Background: During the first wave of the COVID-19 pandemic, the importance of the recognition of vulnerable workers was well-established, but the specific impact of the timing of their recognition remains less understood. Objective: This study evaluates the impact of early recognition of vulnerable healthcare workers (VHCWs) and identifies factors associated with SARS-CoV-2 infection. Methods: We performed a retrospective cohort study at the Virgen Macarena University Hospital (HUVM) in Seville and included employees classified as VHCWs between January 2020 and December 2021. All data, including demographic, occupational, and clinical data, were collected from occupational health records and the Andalusian digital health system. The incidence of COVID-19 was analyzed using descriptive, bivariate statistics, and Cox regression. Results: A total of 471 VHCWs were included. Most of the VHCWs were women (79.8%) with a median age of 50 years. The most common vulnerability criteria were pregnancy (32.9%) and age > 60 (28.7%). During the study period, 58 VHCWs (12.3%) were diagnosed with COVID-19, compared to 18.35% of the general workforce. Recognition of VHCW status after the pandemic was declared was strongly associated with higher infection risk (HR = 48.84; 95% CI: 26.21–90.99; p < 0.001). Conclusions: The timing of vulnerability recognition emerged as the most critical protective factor in this cohort. Healthcare workers whose vulnerability was not proactively identified before the pandemic onset faced a substantially higher risk of infection (HR = 44.68; 95% CI: 26.21–90.99; p < 0.001) compared to those recognized early. These findings underscore that pre-pandemic identification facilitated the immediate implementation of task adaptations and workplace restrictions, effectively mitigating high-risk exposure during the most critical early stages of the crisis.