Health care personnel constitutes the most vulnerable group of professionals, as they are employed in a work context with higher exposure to SARS-CoV-2 infection. This study aims to estimate the prevalence of SARS-CoV-2 infection in health personnel (n = 2858) of two health departments in the Valencian community between March 2020 and April 2021, as well as the sociodemographic and work variables predicting higher infection prevalence in this group. A cross-sectional descriptive study was performed on health workers from the health departments of Torrevieja and Elche-Crevillente of the Valencian Community (Spain). After obtaining the samples, the cases were identified through an active infection diagnostic test (AIDT). The analyzed variables were: sex, age (18–34/35–49/>50 years), professional category, health care, risk service, and AIDT. A total of 2858 staff members were studied. Of them, 55.4% (1582) underwent an AIDT, with 9.7% (277) of positive cases. Infection predominated in the age group of 18 to 34 years, 12.6% (OR = 1.98, 95% CI [1.26, 3.11]); nurses, 12.1% (OR = 1.5, 95% CI [1.00, 2.23]); and at-risk services, 11.4% (OR = 1.3, 95% CI [1.06, 1.81]). A very low positivity rate was identified in the health personnel linked to the health departments analyzed during the 14 months of the study period. Based on our results, prevention strategies could focus more intensively on the most at-risk groups, specifically young nurses who work in at-risk services, mainly in emergency and internal medicine.